[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/15084766/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/15104504/MESO-TP.mergedcluster.txt"

nPatients in clinical file=77, in cluster file=87, common to both=77
[1]  8 77
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
18 25 21 13 
 1  2  3  4 
18 25 21 13 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
13 17 23 24 
 1  2  3  4 
13 17 23 24 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
23 19 16 19 
 1  2  3  4 
23 19 16 19 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
19 12 18 13 15 
 1  2  3  4  5 
19 12 18 13 15 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
32 27 18 
 1  2  3 
32 27 18 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
24 23  6 12 12 
 1  2  3  4  5 
24 23  6 12 12 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
33 23 19 
 1  2  3 
33 23 19 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
14 15 19 27 
 1  2  3  4 
14 15 19 27 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "KARNOFSKY_PERFORMANCE_SCORE"           
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 77 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=63,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'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"                       "75"   
freq.contrast "76"    "76"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 15:'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)"
Variable 16:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 77 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "GENDER"                     
[7] "KARNOFSKY_PERFORMANCE_SCORE"
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
14 25 28  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 25 28  8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 25 28  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 25 28  8 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
42 10 19  2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   42    10    21 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
42 10 19  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   42    10    21 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  3 15
  subtype2  3 22
  subtype3  2 18
  subtype4  3 10
subtype1 subtype2 subtype3 subtype4 
      18       25       20       13 
subtype1 subtype2 subtype3 subtype4 
      15       22       18       10 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       56.38        42.81         8.02        31.20        80.84        91.73 
TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-TS-A7OU TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB 
       10.95        66.54        55.07        22.65        15.02        32.28 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AAC1 TCGA-YS-AA4M TCGA-ZN-A9VS TCGA-ZN-A9VU 
       26.14         1.55        25.94         2.76        33.70        24.30 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 
       11.87        29.10        27.16         1.87        12.72        11.51 
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR TCGA-SH-A7BC 
       18.81         5.19        19.99        13.61        29.42        23.90 
TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI 
       14.76        41.46         9.30        19.43        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
       15.42         8.32        14.99        13.35        14.27         2.50 
TCGA-ZN-A9VQ 
       16.41 

$subtype3
TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4NY TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       12.66        13.61        17.95         5.52        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SH-A7BD 
        3.52        24.89         0.66        28.96         9.76        15.09 
TCGA-TS-A7P1 TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D 
       18.51        27.72         6.48        23.64        23.77        21.44 
TCGA-XT-AASU TCGA-ZN-A9VW 
        4.67         2.76 

$subtype4
TCGA-3H-AB3X TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-AA5Z 
       26.40         6.08        14.73        62.27         2.56        17.72 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-UT-A97Y TCGA-YS-A95B 
        7.99        14.76         8.38        27.75         4.73         1.28 
TCGA-YS-A95C 
        4.37 

subtype1 subtype2 subtype3 subtype4 
    1.55     1.87     0.66     1.28 
subtype1 subtype2 subtype3 subtype4 
   91.73    41.46    28.96    62.27 
subtype1 subtype2 subtype3 subtype4 
   28.67    14.27    16.21     8.38 
[1] "1.6 - 91.7 (28.7)" "1.9 - 41.5 (14.3)" "0.7 - 29.0 (16.2)"
[4] "1.3 - 62.3 (8.4)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        0        6         8        2
  subtype2       3        0        0        4        16        2
  subtype3       2        0        1        4        10        4
  subtype4       1        1        0        2         6        3
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        3        2        1
  STAGE IA         1        0        0        1
  STAGE IB         0        0        1        0
  STAGE II         6        4        4        2
  STAGE III        8       16       10        6
  STAGE IV         2        2        4        3
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3  9  4  1
  subtype2  4  6 12  2
  subtype3  3  8  7  3
  subtype4  4  2  5  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        4        3        4
  T2        9        6        8        2
  T3        4       12        7        5
  T4        1        2        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     4
  subtype2 13  3     9
  subtype3 11  2     4
  subtype4  6  3     4
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          12       13       11        6
  N1           2        3        2        3
  N2+N3        4        9        4        4
[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  8  1
  subtype2 17  0
  subtype3 14  1
  subtype4 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2   17    0
  subtype3   14    1
  subtype4   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        8       17       14       10
  1        1        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"
D1V7, binary
          cls
clus        0  1
  subtype1  1 17
  subtype2  5 20
  subtype3  4 17
  subtype4  5  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   17
  subtype2    5   20
  subtype3    4   17
  subtype4    5    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        5        4        5
  MALE         17       20       17        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"
D1V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        2        1        1 
character(0)

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  4  9
  subtype2  0 16
  subtype3  3 20
  subtype4  4 20
subtype1 subtype2 subtype3 subtype4 
      13       16       23       24 
subtype1 subtype2 subtype3 subtype4 
       9       16       20       20 
$subtype1
TCGA-3H-AB3K TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A4LC TCGA-MQ-A6BQ TCGA-SC-A6LR 
       56.38        17.95         1.87        91.73        66.54        29.42 
TCGA-TS-A7OU TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-YS-A95C TCGA-ZN-A9VS 
       55.07         6.48        14.99        13.35         4.37        33.70 
TCGA-ZN-A9VU 
       24.30 

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

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O7 
       29.10        27.16        26.40         5.52         8.02        11.51 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       18.81        23.31        24.89        19.99        28.96        13.61 
TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7PB TCGA-UD-AABY 
       15.09        14.76        27.75        22.65        32.28        27.72 
TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95B TCGA-ZN-A9VQ 
        8.32        14.27         2.50         1.28        16.41 

$subtype4
TCGA-3H-AB3O TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LM 
       42.81         6.08        31.20        14.73        80.84         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z 
        3.52        10.95        62.27         2.56         9.76        17.72 
TCGA-SH-A7BC TCGA-TS-A7OY TCGA-TS-A7P8 TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY 
       23.90         8.38        15.02        26.14         1.55        15.42 
TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       25.94        23.77        21.44         4.73         4.67         2.76 

subtype1 subtype2 subtype3 subtype4 
    1.87     0.66     1.28     1.55 
subtype1 subtype2 subtype3 subtype4 
   91.73    41.46    32.28    80.84 
subtype1 subtype2 subtype3 subtype4 
  24.300   12.690   18.810   14.875 
[1] "1.9 - 91.7 (24.3)" "0.7 - 41.5 (12.7)" "1.3 - 32.3 (18.8)"
[4] "1.6 - 80.8 (14.9)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        0        7         4        2
  subtype2       2        0        1        3         9        2
  subtype3       3        0        0        3        13        4
  subtype4       2        2        0        3        14        3
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        2        3        2
  STAGE IA         0        0        0        2
  STAGE IB         0        1        0        0
  STAGE II         7        3        3        3
  STAGE III        4        9       13       14
  STAGE IV         2        2        4        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  2  7  2  2
  subtype2  3  5  6  2
  subtype3  3  7 10  3
  subtype4  6  6 10  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        3        3        6
  T2        7        5        7        6
  T3        2        6       10       10
  T4        2        2        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 10  0     3
  subtype2  9  1     5
  subtype3 12  4     6
  subtype4 11  5     7
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          10        9       12       11
  N1           0        1        4        5
  N2+N3        3        5        6        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2  8  0
  subtype3 16  1
  subtype4 16  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2    8    0
  subtype3   16    1
  subtype4   16    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        9        8       16       16
  1        0        0        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  1 12
  subtype2  2 15
  subtype3  6 17
  subtype4  6 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   12
  subtype2    2   15
  subtype3    6   17
  subtype4    6   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        6        6
  MALE         12       15       17       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"
D2V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        1        1        1 
[1] "subtype1" "subtype1" "subtype1"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  4 19
  subtype2  5 13
  subtype3  0 16
  subtype4  2 17
subtype1 subtype2 subtype3 subtype4 
      23       18       16       19 
subtype1 subtype2 subtype3 subtype4 
      19       13       16       17 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 
       56.38        11.87        27.16        17.95         8.02        12.72 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LQ 
       80.84        91.73        24.89        66.54        19.99         9.76 
TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UD-AAC6 
       15.09        55.07        32.28        26.14        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95C TCGA-ZN-A9VS TCGA-ZN-A9VU 
       23.77        14.27         4.37        33.70        24.30 

$subtype2
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       29.10        26.40         5.52        11.51        18.81        23.31 
TCGA-MQ-A6BR TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A9CT TCGA-SH-A9CU 
       62.27        29.42        17.72        23.90        14.76        14.76 
TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-YS-A95B 
       41.46         9.30        15.02        15.42        25.94         1.28 

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

$subtype4
TCGA-3H-AB3S TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH 
       12.66        14.73        17.33        28.96        13.61         7.99 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI 
       27.75        18.51        22.65        19.43        11.77        10.78 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y 
       27.72         6.48         8.32        21.44         2.50         4.73 
TCGA-ZN-A9VQ 
       16.41 

subtype1 subtype2 subtype3 subtype4 
    4.37     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 
   91.73    62.27    42.81    28.96 
subtype1 subtype2 subtype3 subtype4 
  23.770   18.265    4.930   14.730 
[1] "4.4 - 91.7 (23.8)" "1.3 - 62.3 (18.3)" "0.7 - 42.8 (4.9)" 
[4] "2.5 - 29.0 (14.7)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        1        0        7        10        3
  subtype2       0        0        0        3        13        3
  subtype3       1        1        1        3         7        3
  subtype4       4        0        0        3        10        2
D3V3, 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       13        7       10
  STAGE IV         3        3        3        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  2
  subtype2  2  5  8  3
  subtype3  4  5  6  1
  subtype4  4  5  8  2
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        2        4        4
  T2       10        5        5        5
  T3        6        8        6        8
  T4        2        3        1        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     7
  subtype2  5  5     8
  subtype3 11  1     2
  subtype4 11  3     4
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          15        5       11       11
  N1           1        5        1        3
  N2+N3        7        8        2        4
[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  1
  subtype1 14  1
  subtype2 13  0
  subtype3 10  1
  subtype4 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    1
  subtype2   13    0
  subtype3   10    1
  subtype4   12    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       14       13       10       12
  1        1        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"
D3V7, binary
          cls
clus        0  1
  subtype1  3 20
  subtype2  7 12
  subtype3  1 15
  subtype4  4 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   20
  subtype2    7   12
  subtype3    1   15
  subtype4    4   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        7        1        4
  MALE         20       12       15       15
[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, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        1        1        2 
character(0)

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5 14
  subtype2  0 12
  subtype3  4 13
  subtype4  0 13
  subtype5  2 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       12       17       13       15 
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       12       13       13       13 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-MQ-A4KX TCGA-MQ-A4LC 
       56.38        27.16        17.95         8.02        80.84        91.73 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD 
       24.89        66.54        19.99         9.76        29.42        15.09 
TCGA-TS-A7OU TCGA-TS-A7PB TCGA-TS-A8AS TCGA-UT-A88C TCGA-YS-A95C TCGA-ZN-A9VS 
       55.07        32.28        26.14        23.77         4.37        33.70 
TCGA-ZN-A9VU 
       24.30 

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

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4NY TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR 
       29.10        26.40         5.52        18.81        23.31        62.27 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 
       17.72        23.90        14.76        14.76         8.38        41.46 
TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-YS-A95B 
        9.30        15.02        15.42        25.94         1.28 

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

$subtype5
TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH TCGA-TS-A7OZ 
       14.73        17.33        28.96        13.61         7.99        27.75 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UT-A88D 
       22.65        19.43        10.78        27.72         8.32        21.44 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ 
        2.50         4.73        16.41 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.37     1.87     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.73    23.64    62.27    42.81    28.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
   26.14    12.69    17.72     4.67    16.41 
[1] "4.4 - 91.7 (26.1)" "1.9 - 23.6 (12.7)" "1.3 - 62.3 (17.7)"
[4] "0.7 - 42.8 (4.7)"  "2.5 - 29.0 (16.4)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        0        6         8        3
  subtype2       2        0        0        4         6        0
  subtype3       0        0        0        3        11        4
  subtype4       1        1        1        2         6        2
  subtype5       3        0        0        1         9        2
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        2        0        1        3
  STAGE IA         1        0        0        1        0
  STAGE IB         0        0        0        1        0
  STAGE II         6        4        3        2        1
  STAGE III        8        6       11        6        9
  STAGE IV         3        0        4        2        2
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  4  8  5  2
  subtype2  2  6  3  0
  subtype3  1  5  8  3
  subtype4  4  4  4  1
  subtype5  3  2  8  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4        2        1        4        3
  T2        8        6        5        4        2
  T3        5        3        8        4        8
  T4        2        0        3        1        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 12  1     6
  subtype2  8  1     3
  subtype3  5  4     8
  subtype4  9  1     1
  subtype5  8  3     3
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          12        8        5        9        8
  N1           1        1        4        1        3
  N2+N3        6        3        8        1        3
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 10  1
  subtype2 10  0
  subtype3 11  0
  subtype4  8  1
  subtype5 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    1
  subtype2   10    0
  subtype3   11    0
  subtype4    8    1
  subtype5   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       10       10       11        8       10
  1        1        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"
D4V7, binary
          cls
clus        0  1
  subtype1  2 17
  subtype2  2 10
  subtype3  7 11
  subtype4  0 13
  subtype5  4 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   17
  subtype2    2   10
  subtype3    7   11
  subtype4    0   13
  subtype5    4   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        2        2        7        0        4
  MALE         17       10       11       13       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"
D4V8, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype1 subtype4 subtype5 
       3        1        2 
[1] "subtype1" "subtype1" "subtype1"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  4 28
  subtype2  6 20
  subtype3  1 17
subtype1 subtype2 subtype3 
      32       26       18 
subtype1 subtype2 subtype3 
      28       20       17 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4O6 TCGA-MQ-A4LM 
       56.38        11.87        12.66        13.61        14.73         5.19 
TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z 
        3.52         0.66        28.96         2.56         9.76        17.72 
TCGA-SH-A7BC TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       23.90        55.07        18.51        22.65         9.30        19.43 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        26.14         1.55        27.72         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       23.64        14.99        21.44         4.73         4.67         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       16.41        24.30 

$subtype2
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4KX 
       29.10        27.16        17.95         5.52        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        18.81        23.31        17.33        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A9CU 
       62.27        19.99        13.61        29.42        15.09        14.76 
TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95B 
       41.46        15.02        15.42        23.77        14.27         1.28 
TCGA-YS-A95C TCGA-ZN-A9VS 
        4.37        33.70 

$subtype3
TCGA-3H-AB3O TCGA-3H-AB3X TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       42.81        26.40         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ 
       12.72        10.95         7.99        14.76         8.38        27.75 
TCGA-TS-A8AI TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-ZN-A9VW 
       10.78        25.94         8.32        13.35         2.50         2.76 

subtype1 subtype2 subtype3 
    0.66     1.28     1.87 
subtype1 subtype2 subtype3 
   56.38    91.73    42.81 
subtype1 subtype2 subtype3 
  14.860   19.400   10.865 
[1] "0.7 - 56.4 (14.9)" "1.3 - 91.7 (19.4)" "1.9 - 42.8 (10.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       4        1        1        7        15        4
  subtype2       2        0        0        5        16        4
  subtype3       1        1        0        4         9        3
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          4        2        1
  STAGE IA         1        0        1
  STAGE IB         1        0        0
  STAGE II         7        5        4
  STAGE III       15       16        9
  STAGE IV         4        4        3
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  7 10 11  3
  subtype2  5  9  9  3
  subtype3  2  6  8  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7        5        2
  T2       10        9        6
  T3       11        9        8
  T4        3        3        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 17  1    11
  subtype2 12  6     8
  subtype3 13  3     2
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          17       12       13
  N1           1        6        3
  N2+N3       11        8        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 18  1
  subtype2 17  1
  subtype3 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   17    1
  subtype3   14    0
   clus
vv  subtype1 subtype2 subtype3
  0       18       17       14
  1        1        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  4 28
  subtype2  7 20
  subtype3  4 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   28
  subtype2    7   20
  subtype3    4   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        7        4
  MALE         28       20       14
[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"
D5V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        2        1 
[1] "subtype1" "subtype1" "subtype1"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  4 20
  subtype2  3 19
  subtype3  0  6
  subtype4  1 11
  subtype5  3  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       22        6       12       12 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       19        6       11        9 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
       56.38        11.87        13.61         5.19         3.52         0.66 
TCGA-SC-A6LP TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 
        2.56        17.72        23.90        55.07        27.75        18.51 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AV TCGA-UD-AAC4 TCGA-UD-AAC6 
        9.30        19.43        10.78         1.55        23.64        14.99 
TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       21.44         4.73         4.67         2.76        16.41        24.30 

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

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

$subtype4
TCGA-3H-AB3S TCGA-3H-AB3X TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-TS-A7P3 
       12.66        26.40        14.73        19.99         9.76        22.65 
TCGA-TS-A8AF TCGA-TS-A8AS TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-YS-A95B 
       11.77        26.14        27.72         6.48         8.32         1.28 

$subtype5
TCGA-3H-AB3U TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       27.16        80.84        91.73        17.33        24.89        66.54 
TCGA-SC-A6LM TCGA-SH-A7BD TCGA-TS-A7PB TCGA-UT-A88C TCGA-UT-A88E TCGA-ZN-A9VS 
       28.96        15.09        32.28        23.77        14.27        33.70 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     2.50     1.87     1.28    14.27 
subtype1 subtype2 subtype3 subtype4 subtype5 
   56.38    62.27    42.81    27.72    91.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.300   14.890    9.665   13.695   28.060 
[1] "0.7 - 56.4 (14.3)"  "2.5 - 62.3 (14.9)"  "1.9 - 42.8 (9.7)"  
[4] "1.3 - 27.7 (13.7)"  "14.3 - 91.7 (28.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       4        0        1        5        10        4
  subtype2       0        0        0        5        15        3
  subtype3       0        1        0        1         3        1
  subtype4       1        1        0        3         6        1
  subtype5       2        0        0        2         6        2
D6V3, 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       10       15        3        6        6
  STAGE IV         4        3        1        1        2
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  6  7  7  3
  subtype2  3  9  7  3
  subtype3  1  1  4  0
  subtype4  2  4  5  1
  subtype5  2  4  5  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        3        1        2        2
  T2        7        9        1        4        4
  T3        7        7        4        5        5
  T4        3        3        0        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 13  2     7
  subtype2  9  6     7
  subtype3  5  0     1
  subtype4  7  1     4
  subtype5  8  1     2
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          13        9        5        7        8
  N1           2        6        0        1        1
  N2+N3        7        7        1        4        2
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 17  0
  subtype3  5  0
  subtype4  8  0
  subtype5  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   17    0
  subtype3    5    0
  subtype4    8    0
  subtype5    7    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12       17        5        8        7
  1        1        0        0        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1  1 23
  subtype2  7 16
  subtype3  2  4
  subtype4  3  9
  subtype5  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    7   16
  subtype3    2    4
  subtype4    3    9
  subtype5    2   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1        7        2        3        2
  MALE         23       16        4        9       10
[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, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype5"              
clus
subtype1 subtype2 subtype5 
       3        2        1 
[1] "subtype1" "subtype1" "subtype1"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  6 26
  subtype2  4 19
  subtype3  1 18
subtype1 subtype2 subtype3 
      32       23       19 
subtype1 subtype2 subtype3 
      26       19       18 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY 
       56.38        29.10        12.66        27.16        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        8.02        12.72        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BD 
       23.31        24.89        66.54        62.27        19.99        15.09 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P0 TCGA-TS-A8AY TCGA-UD-AABZ 
       14.76        14.76        55.07        41.46        15.42         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VS 
       25.94        13.35        14.27         2.50         4.37        33.70 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       24.30         2.76 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-AA5Z 
       11.87        13.61        17.33         0.66        28.96        17.72 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF 
       27.75        18.51        22.65        19.43        32.28        11.77 
TCGA-UD-AABY TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
       27.72        23.64         8.32        14.99        23.77        21.44 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
        4.73         4.67         1.28         2.76        16.41 

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

subtype1 subtype2 subtype3 
    2.50     0.66     1.55 
subtype1 subtype2 subtype3 
   91.73    32.28    42.81 
subtype1 subtype2 subtype3 
   19.40    17.33    10.95 
[1] "2.5 - 91.7 (19.4)" "0.7 - 32.3 (17.3)" "1.6 - 42.8 (10.9)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0       12        15        4
  subtype2       5        0        1        2        11        4
  subtype3       0        2        0        2        12        3
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          2        5        0
  STAGE IA         0        0        2
  STAGE IB         0        1        0
  STAGE II        12        2        2
  STAGE III       15       11       12
  STAGE IV         4        4        3
[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 10  3
  subtype2  7  4  8  3
  subtype3  3  5  8  2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        7        3
  T2       16        4        5
  T3       10        8        8
  T4        3        3        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 23  5     4
  subtype2 10  1     9
  subtype3  7  4     8
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          23       10        7
  N1           5        1        4
  N2+N3        4        9        8
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 21  1
  subtype2 13  1
  subtype3 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    1
  subtype2   13    1
  subtype3   13    0
   clus
vv  subtype1 subtype2 subtype3
  0       21       13       13
  1        1        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1  8 25
  subtype2  3 20
  subtype3  3 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   25
  subtype2    3   20
  subtype3    3   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        3        3
  MALE         25       20       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        2        1 
character(0)

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  3 11
  subtype2  2 12
  subtype3  4 15
  subtype4  2 25
subtype1 subtype2 subtype3 subtype4 
      14       14       19       27 
subtype1 subtype2 subtype3 subtype4 
      11       12       15       25 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN 
       56.38        11.87        27.16        80.84        91.73        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB TCGA-UT-A88E 
       66.54        19.99        15.09        55.07        32.28        14.27 
TCGA-ZN-A9VS TCGA-ZN-A9VU 
       33.70        24.30 

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

$subtype3
TCGA-3H-AB3O TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       42.81        26.40        17.95         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-TS-A7OY 
       31.20        12.72        10.95         9.76        29.42         8.38 
TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-TS-A8AS TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.02        10.78        26.14         8.32        13.35        23.77 
TCGA-UT-A88D 
       21.44 

$subtype4
TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-NQ-A57I 
       12.66        13.61        14.73         5.19        17.33         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OZ 
       28.96        13.61         2.56        17.72        23.90        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AV 
       18.51        22.65         9.30        19.43        11.77         1.55 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A97Y TCGA-XT-AASU 
       27.72         6.48        23.64        14.99         4.73         4.67 
TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
        1.28         2.76        16.41 

subtype1 subtype2 subtype3 subtype4 
   11.87     2.50     1.87     0.66 
subtype1 subtype2 subtype3 subtype4 
   91.73    62.27    42.81    28.96 
subtype1 subtype2 subtype3 subtype4 
   29.72    15.09    13.35    13.61 
[1] "11.9 - 91.7 (29.7)" "2.5 - 62.3 (15.1)"  "1.9 - 42.8 (13.3)" 
[4] "0.7 - 29.0 (13.6)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0        5         5        2
  subtype2       0        0        0        3        10        2
  subtype3       1        2        0        4         9        3
  subtype4       4        0        1        4        14        4
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        1        4
  STAGE IA         0        0        2        0
  STAGE IB         0        0        0        1
  STAGE II         5        3        4        4
  STAGE III        5       10        9       14
  STAGE IV         2        2        3        4
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  7  3  1
  subtype2  2  5  6  2
  subtype3  4  5  7  2
  subtype4  6  8 10  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        2        4        6
  T2        7        5        5        8
  T3        3        6        7       10
  T4        1        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"
          vv
clus       N0 N1 N2+N3
  subtype1 11  1     2
  subtype2  6  4     4
  subtype3 11  3     5
  subtype4 12  2    10
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11        6       11       12
  N1           1        4        3        2
  N2+N3        2        4        5       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"
D8V6, binary
          cls
clus        0  1
  subtype1  6  1
  subtype2 10  0
  subtype3 15  0
  subtype4 16  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2   10    0
  subtype3   15    0
  subtype4   16    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        6       10       15       16
  1        1        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"
D8V7, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  6  9
  subtype3  3 16
  subtype4  4 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    6    9
  subtype3    3   16
  subtype4    4   23
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        6        3        4
  MALE         13        9       16       23
[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"
D8V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        1        2 
character(0)
