[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/22507181/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/22541489/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 
27 21 16 23 
 1  2  3  4 
27 21 16 23 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
16 19 18 25  9 
 1  2  3  4  5 
16 19 18 25  9 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
 8 24 24  7 
 1  2  3  4 
 8 24 24  7 
[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 21 19 21 
 1  2  3  4 
26 21 19 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
23 12 21 15 16 
 1  2  3  4  5 
23 12 21 15 16 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
21 25 16 25 
 1  2  3  4 
21 25 16 25 
[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 
39 23 23 
 1  2  3 
39 23 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
17 18 16 34 
 1  2  3  4 
17 18 16 34 
[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=70,	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=13,	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 20
  subtype2  2 19
  subtype3  0 15
  subtype4  4 19
subtype1 subtype2 subtype3 subtype4 
      26       21       15       23 
subtype1 subtype2 subtype3 subtype4 
      20       19       15       19 
$subtype1
TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-3H-AB3K TCGA-3U-A98H 
       62.99        20.71        31.20        26.14        56.38        38.01 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LV TCGA-MQ-A6BN 
       17.95         8.02        80.84        91.73         3.52        24.89 
TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P3 
       77.56         0.66        28.96        15.09        55.07        22.65 
TCGA-TS-A7PB TCGA-UD-AAC1 TCGA-UT-A88C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
       32.28        25.94        28.37         2.76         8.58         7.50 
TCGA-ZN-A9VU TCGA-ZN-A9VV 
       32.12        43.04 

$subtype2
TCGA-3H-AB3L TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI 
       11.87        17.62        28.27         1.87        12.72        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-TS-A7P0 TCGA-TS-A7P6 
        5.19        10.95        19.99        23.90        41.46         9.30 
TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88E 
       19.43        11.77        15.42         8.32        13.35        14.27 
TCGA-UT-A88G TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        2.50        16.41        40.37 

$subtype3
TCGA-3H-AB3S TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LJ 
       12.66        29.10        27.16         5.52        11.51        23.31 
TCGA-MQ-A4LP TCGA-SC-A6LN TCGA-SH-A9CU TCGA-TS-A7P1 TCGA-TS-A8AI TCGA-UD-AABZ 
       17.33        13.61        24.07        18.51        10.78         6.48 
TCGA-UD-AAC6 TCGA-XT-AASU TCGA-ZN-A9VW 
       14.99         4.67         2.76 

$subtype4
TCGA-3H-AB3O TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3T TCGA-3H-AB3X 
       42.81        21.83        23.64        27.06        13.61        48.99 
TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BR TCGA-SC-A6LP 
        4.67        24.36         6.08        14.73        68.71         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ 
        9.76        38.40         7.99        14.76         8.38        27.75 
TCGA-TS-A7P8 TCGA-UD-AABY TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C 
       15.02        27.72         4.73         1.28         4.37 

subtype1 subtype2 subtype3 subtype4 
    0.66     1.87     2.76     1.28 
subtype1 subtype2 subtype3 subtype4 
   91.73    41.46    29.10    68.71 
subtype1 subtype2 subtype3 subtype4 
  27.255   14.270   13.610   14.760 
[1] "0.7 - 91.7 (27.3)" "1.9 - 41.5 (14.3)" "2.8 - 29.1 (13.6)"
[4] "1.3 - 68.7 (14.8)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        1        5        10        9
  subtype2       3        0        0        4        13        1
  subtype3       1        0        0        4         8        3
  subtype4       2        1        0        3        14        3
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        3        1        2
  STAGE IA         1        0        0        1
  STAGE IB         1        0        0        0
  STAGE II         5        4        4        3
  STAGE III       10       13        8       14
  STAGE IV         9        1        3        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  4 10  6  7
  subtype2  3  5 11  1
  subtype3  1  6  6  3
  subtype4  6  5  9  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        3        1        6
  T2       10        5        6        5
  T3        6       11        6        9
  T4        7        1        3        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 12  2    11
  subtype2 14  1     6
  subtype3  8  3     3
  subtype4 10  4     9
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          12       14        8       10
  N1           2        1        3        4
  N2+N3       11        6        3        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"
D1V6, binary
          cls
clus        0  1
  subtype1 13  3
  subtype2 13  0
  subtype3 12  0
  subtype4 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    3
  subtype2   13    0
  subtype3   12    0
  subtype4   19    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       13       13       12       19
  1        3        0        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2  4 17
  subtype3  2 14
  subtype4  6 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2    4   17
  subtype3    2   14
  subtype4    6   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        4        2        6
  MALE         23       17       14       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"
D1V8, binary
          cls
clus        0  1
  subtype1 21  6
  subtype2 17  4
  subtype3  9  6
  subtype4 15  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    6
  subtype2   17    4
  subtype3    9    6
  subtype4   15    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       17        9       15
  YES        6        4        6        8
[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
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 
       6        2        3        6 
 [1] "subtype1" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype1" "subtype3"
[13] "subtype1" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     6                                    3
  subtype2                     6                                    0
  subtype3                     6                                    0
  subtype4                     5                                    2
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       17                        1
  subtype2                       15                        0
  subtype3                       10                        0
  subtype4                       15                        1
D1V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       6        6        6        5
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        3        0        0        2
  EPITHELIOID MESOTHELIOMA                   17       15       10       15
  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  7  1  6  1
  subtype2  1  2  3  3
  subtype3  5  0  1  2
  subtype4  4  0  5  5
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        7        1        5        4
  R1        1        2        0        0
  R2        6        3        1        5
  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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  5 11
  subtype2  3 15
  subtype3  1 17
  subtype4  1 23
  subtype5  2  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       18       18       24        9 
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       15       17       23        7 
$subtype1
TCGA-3U-A98E TCGA-3H-AB3K TCGA-3H-AB3U TCGA-LK-A4NW TCGA-MQ-A4LC TCGA-MQ-A6BQ 
       62.99        56.38        27.16        17.95        91.73        77.56 
TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7PB TCGA-UD-AABZ TCGA-UD-AAC6 
       15.09        55.07        18.51        32.28         6.48        14.99 
TCGA-UT-A88C TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
       28.37         8.58        40.37        32.12 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4NY TCGA-LK-A4O7 
       11.87        48.99         4.67        28.27         5.52        11.51 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7P0 
       18.81        23.31        68.71         7.99        14.76        41.46 
TCGA-TS-A7P6 TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-YS-A95B TCGA-ZN-A9VP 
        9.30        15.42        25.94        13.35         1.28         7.50 

$subtype3
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-3H-AB3M TCGA-3U-A98F TCGA-LK-A4NZ TCGA-LK-A4O5 
       12.66        23.64        29.10        17.62         8.02        12.72 
TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-TS-A7P7 TCGA-TS-A8AF 
       17.33        24.89        19.99        28.96        19.43        11.77 
TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UT-A88E TCGA-ZN-A9VQ TCGA-ZN-A9VW 
       10.78        27.72         8.32        14.27        16.41         2.76 

$subtype4
TCGA-3H-AB3O TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS TCGA-UT-A88D 
       42.81        20.71        31.20        21.83        26.14        27.06 
TCGA-3H-AB3T TCGA-3U-A98H TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-MQ-A4KX 
       13.61        38.01         6.08         1.87        14.73        80.84 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SC-A6LP TCGA-SC-A6LQ 
        5.19         3.52        10.95         0.66         2.56         9.76 
TCGA-SH-A7BC TCGA-TS-A7OY TCGA-TS-A7P8 TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.90         8.38        15.02         4.73         4.67         2.76 

$subtype5
TCGA-3U-A98J TCGA-SC-A6LN TCGA-SC-A6LR TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P3 
       24.36        13.61        38.40        24.07        27.75        22.65 
TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VV 
        2.50         4.37        43.04 

subtype1 subtype2 subtype3 subtype4 subtype5 
    6.48     1.28     2.76     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.73    68.71    29.10    80.84    43.04 
subtype1 subtype2 subtype3 subtype4 subtype5 
  30.245   14.055   16.870   12.280   24.070 
[1] "6.5 - 91.7 (30.2)" "1.3 - 68.7 (14.1)" "2.8 - 29.1 (16.9)"
[4] "0.7 - 80.8 (12.3)" "2.5 - 43.0 (24.1)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        0        6         4        5
  subtype2       0        0        0        4        13        2
  subtype3       3        0        0        3         9        3
  subtype4       3        2        1        3        11        5
  subtype5       0        0        0        0         8        1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        0        3        3        0
  STAGE IA         0        0        0        2        0
  STAGE IB         0        0        0        1        0
  STAGE II         6        4        3        3        0
  STAGE III        4       13        9       11        8
  STAGE IV         5        2        3        5        1
[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  1  7  4  4
  subtype2  1  7  8  2
  subtype3  3  6  6  3
  subtype4  7  5  9  3
  subtype5  2  1  5  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        3        7        2
  T2        7        7        6        5        1
  T3        4        8        6        9        5
  T4        4        2        3        3        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 11  0     5
  subtype2  7  4     7
  subtype3 11  2     4
  subtype4 14  3     6
  subtype5  1  1     7
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          11        7       11       14        1
  N1           0        4        2        3        1
  N2+N3        5        7        4        6        7
[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"
D2V6, binary
          cls
clus        0  1
  subtype1  8  2
  subtype2 14  0
  subtype3 11  0
  subtype4 18  1
  subtype5  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    2
  subtype2   14    0
  subtype3   11    0
  subtype4   18    1
  subtype5    6    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        8       14       11       18        6
  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"
D2V7, binary
          cls
clus        0  1
  subtype1  1 15
  subtype2  7 12
  subtype3  4 14
  subtype4  4 21
  subtype5  0  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   15
  subtype2    7   12
  subtype3    4   14
  subtype4    4   21
  subtype5    0    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1        7        4        4        0
  MALE         15       12       14       21        9
[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"
D2V8, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2 13  5
  subtype3 14  4
  subtype4 19  6
  subtype5  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2   13    5
  subtype3   14    4
  subtype4   19    6
  subtype5    7    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       13       14       19        7
  YES        7        5        4        6        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"
D2V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        3        2        3        4 
 [1] "subtype1" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
 [7] "subtype2" "subtype2" "subtype5" "subtype1" "subtype4" "subtype1"
[13] "subtype2" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     2                                    2
  subtype2                     4                                    0
  subtype3                     4                                    2
  subtype4                    10                                    1
  subtype5                     3                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       12                        0
  subtype2                       15                        0
  subtype3                       12                        0
  subtype4                       12                        2
  subtype5                        6                        0
D2V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       2        4        4       10
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        0        2        1
  EPITHELIOID MESOTHELIOMA                   12       15       12       12
  SARCOMATOID MESOTHELIOMA                    0        0        0        2
                                      clus
vv                                     subtype5
  BIPHASIC MESOTHELIOMA                       3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        0
  EPITHELIOID MESOTHELIOMA                    6
  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  2  1  2  2
  subtype2  3  1  4  1
  subtype3  2  1  3  3
  subtype4  8  0  5  3
  subtype5  2  0  1  2
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        2        3        2        8        2
  R1        1        1        1        0        0
  R2        2        4        3        5        1
  RX        2        1        3        3        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  1  7
  subtype2  3 21
  subtype3  1 23
  subtype4  0  6
subtype1 subtype2 subtype3 subtype4 
       8       24       24        6 
subtype1 subtype2 subtype3 subtype4 
       7       21       23        6 
$subtype1
TCGA-3H-AB3O TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98H TCGA-LK-A4NW TCGA-SC-A6LQ 
       42.81        56.38        27.16        38.01        17.95         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC 
       38.40        23.90 

$subtype2
TCGA-3U-A98E TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98F TCGA-LK-A4NY TCGA-LK-A4O2 
       62.99        11.87        13.61        17.62         5.52         1.87 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SH-A9CT 
       11.51        18.81        23.31        17.33        28.96        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A8AF TCGA-UD-AAC1 
       24.07        55.07        41.46        18.51        11.77        25.94 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-YS-A95B TCGA-ZN-A9VQ TCGA-ZN-A9VV TCGA-ZN-A9VW 
       14.99        13.35         1.28        16.41        43.04         2.76 

$subtype3
TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-3H-AB3M TCGA-3U-A98D 
       12.66        20.71        31.20        21.83        29.10         4.67 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NZ TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A6BS 
       28.27        24.36         8.02        14.73        80.84        19.99 
TCGA-SC-A6LN TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       13.61        27.75        22.65        19.43        15.02        32.28 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UT-A97Y TCGA-YS-A95C 
       10.78        15.42        27.72         6.48         4.73         4.37 

$subtype4
TCGA-UD-AAC4 TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-MQ-A4LV TCGA-TS-A7OY TCGA-XT-AASU 
       23.64         6.08        12.72         3.52         8.38         4.67 

subtype1 subtype2 subtype3 subtype4 
    9.76     1.28     4.37     3.52 
subtype1 subtype2 subtype3 subtype4 
   56.38    62.99    80.84    23.64 
subtype1 subtype2 subtype3 subtype4 
  32.585   16.870   19.710    7.230 
[1] "9.8 - 56.4 (32.6)" "1.3 - 63.0 (16.9)" "4.4 - 80.8 (19.7)"
[4] "3.5 - 23.6 (7.2)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE III STAGE IV
  subtype1       0        0        1         5        2
  subtype2       3        0        4        11        6
  subtype3       2        0        4        14        4
  subtype4       0        1        0         5        1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        3        2        0
  STAGE IA         0        0        0        1
  STAGE II         1        4        4        0
  STAGE III        5       11       14        5
  STAGE IV         2        6        4        1
[1] 5 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  1  4  2
  subtype2  3  7  7  6
  subtype3  3  7  9  4
  subtype4  1  2  4  0
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        3        3        1
  T2        1        7        7        2
  T3        4        7        9        4
  T4        2        6        4        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       N0 N1 N2+N3
  subtype1  3  0     5
  subtype2 14  2     7
  subtype3  8  6    10
  subtype4  3  0     3
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0           3       14        8        3
  N1           0        2        6        0
  N2+N3        5        7       10        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0
  subtype1  8
  subtype2 17
  subtype3 16
  subtype4  4
[1] "NOT AVAILABLE: table only has an event [0]"
D3V7, binary
          cls
clus        0  1
  subtype1  1  7
  subtype2  7 17
  subtype3  4 20
  subtype4  1  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2    7   17
  subtype3    4   20
  subtype4    1    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        7        4        1
  MALE          7       17       20        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1  3  5
  subtype2 17  7
  subtype3 20  4
  subtype4  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    5
  subtype2   17    7
  subtype3   20    4
  subtype4    7    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3       17       20        7
  YES        5        7        4        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"
D3V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        5        2        1 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     1                                    2
  subtype2                     8                                    0
  subtype3                     6                                    1
  subtype4                     2                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                        5                        0
  subtype2                       16                        0
  subtype3                       17                        0
  subtype4                        2                        2
D3V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       1        8        6        2
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        0        1        1
  EPITHELIOID MESOTHELIOMA                    5       16       17        2
  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  1  0  2  1
  subtype2  2  1  6  1
  subtype3  6  0  2  4
  subtype4  3  1  1  0
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        1        2        6        3
  R1        0        1        0        1
  R2        2        6        2        1
  RX        1        1        4        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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  0  9
  subtype2  0 11
  subtype3  1  9
  subtype4  1 11
  subtype5  3  6
  subtype6  0 11
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       11       10       12        9       11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       11        9       11        6       11 
$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-AB3O TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-3H-AB3T TCGA-LK-A4O7 TCGA-SC-A6LM 
       42.81        23.64        11.87        13.61        11.51        28.96 
TCGA-SC-A6LQ TCGA-SH-A9CT TCGA-TS-A8AF TCGA-UD-AAC1 TCGA-YS-A95B 
        9.76        14.76        11.77        25.94         1.28 

$subtype3
TCGA-3H-AB3S TCGA-3H-AB3M TCGA-LK-A4NZ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR 
       12.66        29.10         8.02        19.99        13.61        38.40 
TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A8AY TCGA-UT-A97Y 
       27.75        22.65        15.42         4.73 

$subtype4
TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-3U-A98D TCGA-3U-A98I TCGA-3U-A98J 
       20.71        31.20        21.83         4.67        28.27        24.36 
TCGA-LK-A4O6 TCGA-MQ-A4LJ TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-UD-AABY 
       14.73        23.31        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 
       62.99        17.62         5.52        17.33        24.07        55.07 
TCGA-TS-A7P0 TCGA-ZN-A9VQ TCGA-ZN-A9VV 
       41.46        16.41        43.04 

$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-UD-AABZ TCGA-UD-AAC7 TCGA-XT-AASU TCGA-ZN-A9VW 
       18.51         6.48        13.35         4.67         2.76 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.37     1.28     4.73     4.67     5.52     1.87 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   80.84    42.81    38.40    32.28    62.99    18.81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.900   13.610   17.705   22.570   24.070    6.480 
[1] "4.4 - 80.8 (23.9)" "1.3 - 42.8 (13.6)" "4.7 - 38.4 (17.7)"
[4] "4.7 - 32.3 (22.6)" "5.5 - 63.0 (24.1)" "1.9 - 18.8 (6.5)" 
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  2
  subtype5  8  1
  subtype6 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2    6    5
  subtype3    7    3
  subtype4   10    2
  subtype5    8    1
  subtype6   10    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         6        6        7       10        8       10
  YES        3        5        3        2        1        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" "subtype4" "subtype4" "subtype2" "subtype1" "subtype3"
 [7] "subtype6" "subtype6" "subtype6" "subtype4" "subtype2" "subtype1"
[13] "subtype6" "subtype6" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype1" "subtype4" "subtype6" "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  4 16
  subtype3  1 17
  subtype4  2 19
subtype1 subtype2 subtype3 subtype4 
      26       20       18       21 
subtype1 subtype2 subtype3 subtype4 
      21       16       17       19 
$subtype1
TCGA-3U-A98E TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U 
       62.99        26.14        23.64        56.38        11.87        27.16 
TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       38.01        17.95         8.02        12.72        80.84        91.73 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-TS-A7OU 
       24.89        77.56        19.99         9.76        15.09        55.07 
TCGA-TS-A7PB TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95C TCGA-ZN-A9VO 
       32.28        14.99        28.37        14.27         4.37         8.58 
TCGA-ZN-A9VS TCGA-ZN-A9VU 
       40.37        32.12 

$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-SH-A7BC TCGA-SH-A9CT 
       18.81        23.31        68.71        38.40        23.90        14.76 
TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UD-AAC1 
       24.07        41.46         9.30        15.02        15.42        25.94 
TCGA-YS-A95B TCGA-ZN-A9VP 
        1.28         7.50 

$subtype3
TCGA-3H-AB3O TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-3H-AB3T TCGA-3U-A98I 
       42.81        20.71        31.20        21.83        13.61        28.27 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I 
        6.08         1.87         5.19         3.52        10.95         0.66 
TCGA-SC-A6LP TCGA-TS-A7OY TCGA-UD-AAC7 TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VW 
        2.56         8.38        13.35         4.67         2.76         2.76 

$subtype4
TCGA-3H-AB3S TCGA-UT-A88D TCGA-3U-A98F TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM 
       12.66        27.06        17.62        14.73        17.33        28.96 
TCGA-SC-A6LN TCGA-SH-A7BH TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 
       13.61         7.99        27.75        18.51        22.65        19.43 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UT-A88G 
       11.77        10.78        27.72         6.48         8.32         2.50 
TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        4.73        16.41        43.04 

subtype1 subtype2 subtype3 subtype4 
    4.37     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 
   91.73    68.71    42.81    43.04 
subtype1 subtype2 subtype3 subtype4 
  25.515   21.060    7.230   16.410 
[1] "4.4 - 91.7 (25.5)" "1.3 - 68.7 (21.1)" "0.7 - 42.8 (7.2)" 
[4] "2.5 - 43.0 (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        2
  subtype3       1        1        1        3         7        6
  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        2        6        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  2
  subtype3  4  5  6  4
  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        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 15  1    10
  subtype2  5  5    10
  subtype3 12  1     4
  subtype4 12  3     5
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          15        5       12       12
  N1           1        5        1        3
  N2+N3       10       10        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"
D5V6, binary
          cls
clus        0  1
  subtype1 16  2
  subtype2 15  0
  subtype3 13  1
  subtype4 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    2
  subtype2   15    0
  subtype3   13    1
  subtype4   13    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       16       15       13       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 14
  subtype3  1 18
  subtype4  4 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   22
  subtype2    7   14
  subtype3    1   18
  subtype4    4   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        7        1        4
  MALE         22       14       18       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 19  7
  subtype2 14  6
  subtype3 15  4
  subtype4 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    7
  subtype2   14    6
  subtype3   15    4
  subtype4   14    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        19       14       15       14
  YES        7        6        4        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" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [7] "subtype4" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype4" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     3                                    3
  subtype2                     2                                    0
  subtype3                    10                                    1
  subtype4                     8                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       20                        0
  subtype2                       19                        0
  subtype3                        6                        2
  subtype4                       12                        0
D5V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       3        2       10        8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        3        0        1        1
  EPITHELIOID MESOTHELIOMA                   20       19        6       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  4  2
  subtype3  5  0  5  1
  subtype4  2  0  2  6
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        7        3        5        2
  R1        2        1        0        0
  R2        4        4        5        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 17
  subtype2  0 12
  subtype3  4 16
  subtype4  0 14
  subtype5  2 14
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       12       20       14       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       12       16       14       14 
$subtype1
TCGA-3U-A98E TCGA-TS-A8AS TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98H TCGA-LK-A4NW 
       62.99        26.14        56.38        27.16        38.01        17.95 
TCGA-LK-A4NZ TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
        8.02        80.84        91.73        24.89        77.56        19.99 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB TCGA-UT-A88C 
        9.76        38.40        15.09        55.07        32.28        28.37 
TCGA-UT-A88E TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
       14.27         4.37         8.58        40.37        32.12 

$subtype2
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 
       12.66        23.64        11.87         1.87        12.72        11.51 
TCGA-TS-A7P1 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 
       18.51        11.77        10.78         6.48        14.99        13.35 

$subtype3
TCGA-SC-AA5Z TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4NY 
       21.83        29.10        48.99         4.67        24.36         5.52 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A9CT TCGA-SH-A9CU 
       18.81        23.31        68.71        23.90        14.76        24.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UD-AAC1 
        8.38        41.46         9.30        15.02        15.42        25.94 
TCGA-YS-A95B TCGA-ZN-A9VP 
        1.28         7.50 

$subtype4
TCGA-3H-AB3O TCGA-3U-A98G TCGA-LK-A4O4 TCGA-3H-AB3T TCGA-3U-A98I TCGA-LK-A4O0 
       42.81        20.71        31.20        13.61        28.27         6.08 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SC-A6LP TCGA-XT-AASU 
        5.19         3.52        10.95         0.66         2.56         4.67 
TCGA-YS-AA4M TCGA-ZN-A9VW 
        2.76         2.76 

$subtype5
TCGA-UT-A88D TCGA-3U-A98F TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN 
       27.06        17.62        14.73        17.33        28.96        13.61 
TCGA-SH-A7BH TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-UD-AABY TCGA-UD-AAC5 
        7.99        27.75        22.65        19.43        27.72         8.32 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        2.50         4.73        16.41        43.04 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.37     1.87     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.73    23.64    68.71    42.81    43.04 
subtype1 subtype2 subtype3 subtype4 subtype5 
  28.370   12.265   20.320    5.635   17.475 
[1] "4.4 - 91.7 (28.4)" "1.9 - 23.6 (12.3)" "1.3 - 68.7 (20.3)"
[4] "0.7 - 42.8 (5.6)"  "2.5 - 43.0 (17.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        1        0        6         8        6
  subtype2       1        0        0        4         6        1
  subtype3       0        0        0        3        14        4
  subtype4       1        1        1        2         6        4
  subtype5       3        0        0        1        11        1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          2        1        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        1        4        4        1
[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  5  8  5  5
  subtype2  1  6  3  1
  subtype3  1  6 10  3
  subtype4  4  4  4  3
  subtype5  3  2 10  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        5        1        1        4        3
  T2        8        6        6        4        2
  T3        5        3       10        4       10
  T4        5        1        3        3        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 13  1     9
  subtype2  7  2     3
  subtype3  5  4    11
  subtype4 10  1     2
  subtype5  9  2     4
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          13        7        5       10        9
  N1           1        2        4        1        2
  N2+N3        9        3       11        2        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 13  2
  subtype2  9  0
  subtype3 14  0
  subtype4 10  1
  subtype5 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    2
  subtype2    9    0
  subtype3   14    0
  subtype4   10    1
  subtype5   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13        9       14       10       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 20
  subtype2  2 10
  subtype3  7 14
  subtype4  0 15
  subtype5  4 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   20
  subtype2    2   10
  subtype3    7   14
  subtype4    0   15
  subtype5    4   12
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        3        2        7        0        4
  MALE         20       10       14       15       12
[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 16  7
  subtype2  7  5
  subtype3 15  5
  subtype4 13  2
  subtype5 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    7
  subtype2    7    5
  subtype3   15    5
  subtype4   13    2
  subtype5   11    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        16        7       15       13       11
  YES        7        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" "subtype5" "subtype3" "subtype5" "subtype5" "subtype1"
 [7] "subtype5" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype5" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     2                                    2
  subtype2                     1                                    1
  subtype3                     2                                    0
  subtype4                    10                                    1
  subtype5                     8                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       19                        0
  subtype2                       10                        0
  subtype3                       19                        0
  subtype4                        2                        2
  subtype5                        7                        0
D6V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       2        1        2       10
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        1        0        1
  EPITHELIOID MESOTHELIOMA                   19       10       19        2
  SARCOMATOID MESOTHELIOMA                    0        0        0        2
                                      clus
vv                                     subtype5
  BIPHASIC MESOTHELIOMA                       8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1
  EPITHELIOID MESOTHELIOMA                    7
  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  2
  subtype2  1  1  4  1
  subtype3  2  1  4  2
  subtype4  5  0  2  1
  subtype5  2  0  2  5
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7        1        2        5        2
  R1        1        1        1        0        0
  R2        3        4        4        2        2
  RX        2        1        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  1 19
  subtype2  3 21
  subtype3  1 15
  subtype4  7 18
subtype1 subtype2 subtype3 subtype4 
      20       24       16       25 
subtype1 subtype2 subtype3 subtype4 
      19       21       15       18 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4O2 TCGA-LK-A4O7 
       56.38        29.10         4.67        24.36         1.87        11.51 
TCGA-MQ-A4LI TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P0 TCGA-TS-A7P7 
       18.81        14.76        24.07        55.07        41.46        19.43 
TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G 
       10.78         6.48        25.94         8.32        13.35         2.50 
TCGA-ZN-A9VP TCGA-ZN-A9VW 
        7.50         2.76 

$subtype2
TCGA-3H-AB3S TCGA-3U-A98G TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-3H-AB3T 
       12.66        20.71        21.83        23.64        11.87        13.61 
TCGA-3U-A98F TCGA-3U-A98I TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-NQ-A57I 
       17.62        28.27         5.19        17.33         3.52         0.66 
TCGA-SC-A6LM TCGA-SH-A7BC TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7PB 
       28.96        23.90        18.51        22.65         9.30        32.28 
TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC6 TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       11.77        27.72        14.99         4.73        16.41        32.12 

$subtype3
TCGA-3H-AB3O TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-UT-A88D TCGA-3H-AB3X TCGA-3U-A98H 
       42.81        31.20        26.14        27.06        48.99        38.01 
TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BL TCGA-SC-A6LP TCGA-SH-A7BH 
        6.08        12.72        14.73        10.95         2.56         7.99 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-XT-AASU TCGA-YS-AA4M 
        8.38        27.75         4.67         2.76 

$subtype4
TCGA-3U-A98E TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-MQ-A4KX 
       62.99        27.16        17.95         5.52         8.02        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
       91.73        23.31        24.89        77.56        68.71        19.99 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7P8 TCGA-TS-A8AY 
       13.61         9.76        38.40        15.09        15.02        15.42 
TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VS 
       28.37        14.27         1.28         4.37         8.58        40.37 
TCGA-ZN-A9VV 
       43.04 

subtype1 subtype2 subtype3 subtype4 
    1.87     0.66     2.56     1.28 
subtype1 subtype2 subtype3 subtype4 
   56.38    32.28    48.99    91.73 
subtype1 subtype2 subtype3 subtype4 
  14.055   17.475   13.725   19.990 
[1] "1.9 - 56.4 (14.1)" "0.7 - 32.3 (17.5)" "2.6 - 49.0 (13.7)"
[4] "1.3 - 91.7 (20.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        0        6        10        4
  subtype2       4        0        1        3        13        4
  subtype3       0        2        0        3         8        3
  subtype4       2        0        0        4        14        5
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        4        0        2
  STAGE IA         0        0        2        0
  STAGE IB         0        1        0        0
  STAGE II         6        3        3        4
  STAGE III       10       13        8       14
  STAGE IV         4        4        3        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  1  8  8  4
  subtype2  5  6  9  4
  subtype3  3  4  8  1
  subtype4  5  8  7  4
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        5        3        5
  T2        8        6        4        8
  T3        8        9        8        7
  T4        4        4        1        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"
          vv
clus       N0 N1 N2+N3
  subtype1 11  2     7
  subtype2 13  0    10
  subtype3 10  3     2
  subtype4 10  5    10
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11       13       10       10
  N1           2        0        3        5
  N2+N3        7       10        2       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 15  0
  subtype2 16  0
  subtype3 11  1
  subtype4 15  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    0
  subtype2   16    0
  subtype3   11    1
  subtype4   15    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       15       16       11       15
  1        0        0        1        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"
D7V7, binary
          cls
clus        0  1
  subtype1  4 17
  subtype2  2 23
  subtype3  3 13
  subtype4  7 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   17
  subtype2    2   23
  subtype3    3   13
  subtype4    7   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        2        3        7
  MALE         17       23       13       18
[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"
D7V8, binary
          cls
clus        0  1
  subtype1 15  5
  subtype2 18  7
  subtype3 13  3
  subtype4 16  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    5
  subtype2   18    7
  subtype3   13    3
  subtype4   16    9
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        15       18       13       16
  YES        5        7        3        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"
D7V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     3                                    1
  subtype2                    11                                    2
  subtype3                     6                                    1
  subtype4                     3                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       17                        0
  subtype2                       11                        1
  subtype3                        8                        1
  subtype4                       21                        0
D7V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       3       11        6        3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        2        1        1
  EPITHELIOID MESOTHELIOMA                   17       11        8       21
  SARCOMATOID MESOTHELIOMA                    0        1        1        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  2  1  3  4
  subtype2  2  0  6  2
  subtype3  4  1  2  2
  subtype4  9  1  4  3
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        2        2        4        9
  R1        1        0        1        1
  R2        3        6        2        4
  RX        4        2        2        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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  3 25
  subtype2  3 21
  subtype3  0  6
  subtype4  2 11
  subtype5  4 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       24        6       13       14 
subtype1 subtype2 subtype3 subtype4 subtype5 
      25       21        6       11       10 
$subtype1
TCGA-3U-A98G TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L 
       20.71        21.83        23.64        27.06        56.38        11.87 
TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I TCGA-3U-A98J TCGA-MQ-A4LM 
       13.61         4.67        17.62        28.27        24.36         5.19 
TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LP TCGA-SH-A7BC TCGA-TS-A7OU TCGA-TS-A7OZ 
        3.52         0.66         2.56        23.90        55.07        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-UD-AAC6 TCGA-UT-A97Y 
       18.51         9.30        19.43        10.78        14.99         4.73 
TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU 
        4.67         2.76        16.41        32.12 

$subtype2
TCGA-LK-A4O4 TCGA-3H-AB3M TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ 
       31.20        29.10        38.01        17.95         5.52         8.02 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SC-A6LR 
       11.51        18.81        23.31        68.71        13.61        38.40 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AY 
        7.99        14.76        24.07        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         7.50         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-TS-A8AS TCGA-3H-AB3X TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LQ 
       12.66        26.14        48.99        14.73        19.99         9.76 
TCGA-TS-A7P3 TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-YS-A95B 
       22.65        11.77        27.72         6.48         8.32         1.28 
TCGA-ZN-A9VV 
       43.04 

$subtype5
TCGA-3U-A98E TCGA-3H-AB3U TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LP TCGA-MQ-A6BN 
       62.99        27.16        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 
       77.56        28.96        15.09        32.28        28.37        14.27 
TCGA-ZN-A9VO TCGA-ZN-A9VS 
        8.58        40.37 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     2.50     1.87     1.28     8.58 
subtype1 subtype2 subtype3 subtype4 subtype5 
   56.38    68.71    42.81    48.99    91.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.015   15.220    9.665   14.730   28.665 
[1] "0.7 - 56.4 (17.0)" "2.5 - 68.7 (15.2)" "1.9 - 42.8 (9.7)" 
[4] "1.3 - 49.0 (14.7)" "8.6 - 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 22  7
  subtype2 18  6
  subtype3  5  1
  subtype4  8  5
  subtype5  9  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    7
  subtype2   18    6
  subtype3    5    1
  subtype4    8    5
  subtype5    9    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        22       18        5        8        9
  YES        7        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  8 30
  subtype2  1 21
  subtype3  3 20
subtype1 subtype2 subtype3 
      38       22       23 
subtype1 subtype2 subtype3 
      30       21       20 
$subtype1
TCGA-3H-AB3S TCGA-3U-A98E TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U 
       12.66        62.99        56.38        11.87        29.10        27.16 
TCGA-3H-AB3X TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O7 
       48.99        24.36         5.52         8.02        12.72        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       80.84        91.73        18.81        23.31        24.89        77.56 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       68.71        19.99        15.09        14.76        24.07        55.07 
TCGA-TS-A7P0 TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-UT-A88C 
       41.46        15.42         6.48        25.94        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS 
       14.27         2.50         4.37         8.58         7.50        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       32.12         2.76 

$subtype2
TCGA-3H-AB3O TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98H 
       42.81        31.20        26.14        13.61         4.67        38.01 
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A6BL 
       17.95         6.08         1.87        14.73         5.19        10.95 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-TS-A7OY 
       13.61         2.56         9.76        38.40        23.90         8.38 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-UD-AAC5 
       22.65        15.02        10.78         8.32 

$subtype3
TCGA-3U-A98G TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3U-A98F TCGA-3U-A98I 
       20.71        21.83        23.64        27.06        17.62        28.27 
TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SC-A6LM TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P6 
       17.33         0.66        28.96        27.75        18.51         9.30 
TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC6 TCGA-UT-A97Y 
       19.43        32.28        11.77        27.72        14.99         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        4.67         1.28         2.76        16.41        43.04 

subtype1 subtype2 subtype3 
    2.50     1.87     0.66 
subtype1 subtype2 subtype3 
   91.73    42.81    43.04 
subtype1 subtype2 subtype3 
   21.65    13.61    18.51 
[1] "2.5 - 91.7 (21.6)" "1.9 - 42.8 (13.6)" "0.7 - 43.0 (18.5)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0       12        19        6
  subtype2       2        2        0        2        13        4
  subtype3       3        0        1        2        11        6
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          2        2        3
  STAGE IA         0        2        0
  STAGE IB         0        0        1
  STAGE II        12        2        2
  STAGE III       19       13       11
  STAGE IV         6        4        6
[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 13  5
  subtype2  5  6  8  3
  subtype3  5  4  9  5
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        5        5
  T2       16        6        4
  T3       13        8        9
  T4        5        3        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 23  5    10
  subtype2  9  4    10
  subtype3 10  1     9
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          23        9       10
  N1           5        4        1
  N2+N3       10       10        9
[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 26  2
  subtype2 17  0
  subtype3 12  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    2
  subtype2   17    0
  subtype3   12    1
   clus
vv  subtype1 subtype2 subtype3
  0       26       17       12
  1        2        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1  9 30
  subtype2  3 20
  subtype3  3 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   30
  subtype2    3   20
  subtype3    3   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        3        3
  MALE         30       20       20
[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 26 12
  subtype2 16  7
  subtype3 18  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   12
  subtype2   16    7
  subtype3   18    5
     clus
vv    subtype1 subtype2 subtype3
  NO        26       16       18
  YES       12        7        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                     8                                    1
  subtype3                    10                                    3
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       35                        0
  subtype2                       12                        2
  subtype3                       10                        0
D9V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3
  BIPHASIC MESOTHELIOMA                       3        8       10
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        1        3
  EPITHELIOID MESOTHELIOMA                   35       12       10
  SARCOMATOID MESOTHELIOMA                    0        2        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  9  3  4  5
  subtype2  4  0  3  4
  subtype3  3  0  7  2
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        9        4        3
  R1        3        0        0
  R2        4        3        7
  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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1  5 12
  subtype2  3 14
  subtype3  1 15
  subtype4  3 30
subtype1 subtype2 subtype3 subtype4 
      17       17       16       33 
subtype1 subtype2 subtype3 subtype4 
      12       14       15       30 
$subtype1
TCGA-3U-A98E TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A4KX TCGA-MQ-A4LC 
       62.99        56.38        11.87        27.16        80.84        91.73 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB 
       24.89        77.56        19.99        15.09        55.07        32.28 
TCGA-UT-A88C TCGA-UT-A88E TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
       28.37        14.27         8.58        40.37        32.12 

$subtype2
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI 
       29.10        48.99        24.36         5.52        11.51        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A8AY 
       23.31        68.71        14.76        24.07        41.46        15.42 
TCGA-UD-AAC1 TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VP TCGA-ZN-A9VW 
       25.94         2.50         4.37         7.50         2.76 

$subtype3
TCGA-3H-AB3O TCGA-LK-A4O4 TCGA-TS-A8AS TCGA-UT-A88D TCGA-3U-A98H TCGA-LK-A4NW 
       42.81        31.20        26.14        27.06        38.01        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SC-A6LQ 
        8.02         6.08         1.87        12.72        10.95         9.76 
TCGA-SC-A6LR TCGA-TS-A7OY TCGA-TS-A7P8 TCGA-UD-AAC7 
       38.40         8.38        15.02        13.35 

$subtype4
TCGA-3H-AB3S TCGA-3U-A98G TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-3H-AB3T TCGA-3U-A98D 
       12.66        20.71        21.83        23.64        13.61         4.67 
TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-NQ-A57I 
       17.62        28.27        14.73         5.19        17.33         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BC TCGA-TS-A7OZ TCGA-TS-A7P1 
       28.96        13.61         2.56        23.90        27.75        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABY 
       22.65         9.30        19.43        11.77        10.78        27.72 
TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
        6.48         8.32        14.99         4.73         4.67         1.28 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        2.76        16.41        43.04 

subtype1 subtype2 subtype3 subtype4 
    8.58     2.50     1.87     0.66 
subtype1 subtype2 subtype3 subtype4 
   91.73    68.71    42.81    43.04 
subtype1 subtype2 subtype3 subtype4 
  32.120   18.810   14.185   14.730 
[1] "8.6 - 91.7 (32.1)" "2.5 - 68.7 (18.8)" "1.9 - 42.8 (14.2)"
[4] "0.7 - 43.0 (14.7)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0        5         6        4
  subtype2       0        0        0        3        13        2
  subtype3       0        2        0        4         7        3
  subtype4       5        0        1        4        17        7
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        0        5
  STAGE IA         0        0        2        0
  STAGE IB         0        0        0        1
  STAGE II         5        3        4        4
  STAGE III        6       13        7       17
  STAGE IV         4        2        3        7
[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  4  3
  subtype2  2  5  9  2
  subtype3  3  5  5  2
  subtype4  7  9 12  6
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        2        3        7
  T2        7        5        5        9
  T3        4        9        5       12
  T4        3        2        2        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"
          vv
clus       N0 N1 N2+N3
  subtype1 11  1     5
  subtype2  7  4     6
  subtype3  9  2     5
  subtype4 15  3    13
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11        7        9       15
  N1           1        4        2        3
  N2+N3        5        6        5       13
[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  8  2
  subtype2 13  0
  subtype3 13  0
  subtype4 21  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    2
  subtype2   13    0
  subtype3   13    0
  subtype4   21    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        8       13       13       21
  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 15
  subtype2  6 12
  subtype3  3 13
  subtype4  4 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   15
  subtype2    6   12
  subtype3    3   13
  subtype4    4   30
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        6        3        4
  MALE         15       12       13       30
[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 12  5
  subtype2 13  4
  subtype3 11  5
  subtype4 24 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    5
  subtype2   13    4
  subtype3   11    5
  subtype4   24   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        12       13       11       24
  YES        5        4        5       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        4        2        5 
 [1] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
 [7] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype4"
[13] "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     1                                    1
  subtype2                     3                                    0
  subtype3                     2                                    1
  subtype4                    15                                    3
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       15                        0
  subtype2                       15                        0
  subtype3                       12                        1
  subtype4                       15                        1
D10V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       1        3        2       15
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        0        1        3
  EPITHELIOID MESOTHELIOMA                   15       15       12       15
  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  5  1  1  1
  subtype2  4  1  1  3
  subtype3  4  1  4  1
  subtype4  3  0  8  6
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        5        4        4        3
  R1        1        1        1        0
  R2        1        1        4        8
  RX        1        3        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"
