[1] "ofn"        "-oTFPPP-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/FPPP-TP/22506420/FPPP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/FPPP-TP/22538209/FPPP-TP.mergedcluster.txt"

nPatients in clinical file=38, in cluster file=23, common to both=23
[1]  4 23
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 4 5 6 7 
5 4 3 3 4 1 3 
1 2 3 4 5 7 
5 4 3 3 4 3 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
2 4 4 6 4 3 
2 3 4 5 6 
4 4 6 4 3 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 3 
6 9 8 
1 2 3 
6 9 8 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
5 6 3 3 4 2 
1 2 3 4 5 
5 6 3 3 4 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "NUMBER_OF_LYMPH_NODES"               
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 23 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=3,	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:'TUMOR_TISSUE_SITE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=2,	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=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "KARNOFSKY_PERFORMANCE_SCORE is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            100     80     
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "YEAR_OF_TOBACCO_SMOKING_ONSET is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            1955    1976   
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RESIDUAL_TUMOR excluded in the analysis because there is no case of (both >= 3) in the table below"
              R0      RX     
freq.values   "2"     "4"    
freq.contrast "4"     "2"    
both >= 3     "FALSE" "FALSE"
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "21"                  
freq.contrast "21"               "2"                   
both >= 3     "FALSE"            "FALSE"               
[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 23 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"           "TUMOR_TISSUE_SITE"       
 [3] "PATHOLOGIC_STAGE"         "PATHOLOGY_T_STAGE"       
 [5] "PATHOLOGY_N_STAGE"        "GENDER"                  
 [7] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "NUMBER_PACK_YEARS_SMOKED" "NUMBER_OF_LYMPH_NODES"   
[11] "RACE"                    
YEARS_TO_BIRTH, nv=16, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGIC_STAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 5  7  5  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    5     7     7 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 5  7  5  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    5     7     7 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
10  3  1 
[1] "table(vv)"
vv
   N0 N1+N2 
   10     4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
10  3  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 10

$Class1_nSamples
[1] 4

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   10     4 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=11, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=4, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=2, binary=FALSE, numeric=TRUE
RACE, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MIRSEQ_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 5 0
  subtype2 4 0
  subtype3 3 0
  subtype4 2 1
  subtype5 4 0
  subtype7 1 2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       5        4        3        3        4        3 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       0        0        0        1        0        2 
$subtype1
TCGA-44-6146 TCGA-A6-5656 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6781 
        9.93        32.91        20.61        20.12        19.66 

$subtype2
TCGA-44-6147 TCGA-A7-A26E TCGA-A7-A0DB TCGA-A7-A26J 
       27.78        31.36        33.11        20.61 

$subtype3
TCGA-44-6775 TCGA-BK-A0CA TCGA-BK-A26L 
       23.18        34.98        24.13 

$subtype4
TCGA-A7-A13D TCGA-A7-A13E TCGA-BK-A139 
       31.73        20.19        10.16 

$subtype5
TCGA-B2-5635 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
       10.36        32.61        35.90        11.77 

$subtype7
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       40.08         7.33         2.66 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
    9.93    20.61    23.18    10.16    10.36     2.66 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
   32.91    33.11    34.98    31.73    35.90    40.08 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
   20.12    29.57    24.13    20.19    22.19     7.33 
[1] "9.9 - 32.9 (20.1)"  "20.6 - 33.1 (29.6)" "23.2 - 35.0 (24.1)"
[4] "10.2 - 31.7 (20.2)" "10.4 - 35.9 (22.2)" "2.7 - 40.1 (7.3)"  
D1V2, continuous
          vv
clus       BLADDER BREAST COLON ENDOMETRIAL KIDNEY LUNG
  subtype1       0      0     4           0      0    1
  subtype2       0      3     0           0      0    1
  subtype3       0      0     0           2      0    1
  subtype4       0      2     0           1      0    0
  subtype5       0      0     0           0      4    0
  subtype7       3      0     0           0      0    0
D1V3, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  BLADDER            0        0        0        0        0        3
  BREAST             0        3        0        2        0        0
  COLON              4        0        0        0        0        0
  ENDOMETRIAL        0        0        2        1        0        0
  KIDNEY             0        0        0        0        4        0
  LUNG               1        1        1        0        0        0
[1] 6 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       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        0        0        0         2         1         0
  subtype2       0        1        0        0         2         0         0
  subtype3       0        0        1        0         0         0         0
  subtype4       0        0        0        0         1         1         0
  subtype5       3        0        0        1         0         0         0
  subtype7       1        0        0        0         0         0         1
          vv
clus       STAGE IIIA STAGE IIIC STAGE IV
  subtype1          0          1        0
  subtype2          1          0        0
  subtype3          0          0        0
  subtype4          0          0        0
  subtype5          0          0        0
  subtype7          0          0        1
D1V4, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       5        4        1        2        4        3 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype5" "subtype5"
[13] "subtype5" "subtype7" "subtype7" "subtype7"
            clus
vv           subtype1 subtype2 subtype5 subtype7
  STAGE I           1        0        3        1
  STAGE IA          0        1        0        0
  STAGE II          0        0        1        0
  STAGE IIA         2        2        0        0
  STAGE IIB         1        0        0        0
  STAGE III         0        0        0        1
  STAGE IIIA        0        1        0        0
  STAGE IIIC        1        0        0        0
  STAGE IV          0        0        0        1
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  0  1     4
  subtype2  1  2     1
  subtype3  0  1     0
  subtype4  0  2     0
  subtype5  3  1     0
  subtype7  1  0     2
D1V5, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       5        4        1        2        4        3 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype5" "subtype5"
[13] "subtype5" "subtype7" "subtype7" "subtype7"
       clus
vv      subtype1 subtype2 subtype5 subtype7
  T1           0        1        3        1
  T2           1        2        1        0
  T3+T4        4        1        0        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  4     1
  subtype2  2     1
  subtype3  1     0
  subtype4  1     1
  subtype5  1     0
  subtype7  1     1
D1V6, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
[4] "subtype5"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       5        3        1        2        1        2 
[1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[8] "subtype2"
       clus
vv      subtype1 subtype2
  N0           4        2
  N1+N2        1        1
[1] 2 2
[1] FALSE
D1V7, binary
          cls
clus       0 1
  subtype1 1 4
  subtype2 4 0
  subtype3 3 0
  subtype4 3 0
  subtype5 0 4
  subtype7 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    4
  subtype2    4    0
  subtype3    3    0
  subtype4    3    0
  subtype5    0    4
  subtype7    1    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  FEMALE        1        4        3        3        0        1
  MALE          4        0        0        0        4        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"
D1V8, binary
          cls
clus       0 1
  subtype1 5 0
  subtype2 2 2
  subtype3 2 1
  subtype4 2 1
  subtype5 2 0
  subtype7 1 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    2    2
  subtype3    2    1
  subtype4    2    1
  subtype5    2    0
  subtype7    1    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  NO         5        2        2        2        2        1
  YES        0        2        1        1        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                    2                             2
  subtype2                    0                             0
  subtype3                    0                             0
  subtype4                    0                             0
  subtype5                    0                             0
  subtype7                    0                             0
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       0
  subtype4                                       1
  subtype5                                       0
  subtype7                                       0
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                             0                              0
  subtype2                             2                              1
  subtype3                             0                              0
  subtype4                             2                              0
  subtype5                             0                              0
  subtype7                             0                              0
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                 0
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 4
  subtype7                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                  0
  subtype2                                                  1
  subtype3                                                  1
  subtype4                                                  0
  subtype5                                                  0
  subtype7                                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID
  subtype1                            1                             0
  subtype2                            0                             0
  subtype3                            0                             1
  subtype4                            0                             0
  subtype5                            0                             0
  subtype7                            0                             0
          vv
clus       MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)
  subtype1                                                   0
  subtype2                                                   0
  subtype3                                                   0
  subtype4                                                   0
  subtype5                                                   0
  subtype7                                                   2
          vv
clus       SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                                 0
  subtype2                                 0
  subtype3                                 1
  subtype4                                 0
  subtype5                                 0
  subtype7                                 0
D1V9, multiclass
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       5        4        3        3        4        2 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype3" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype4" "subtype4"
[13] "subtype2" "subtype5" "subtype5" "subtype5" "subtype3" "subtype4"
[19] "subtype3"
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                                      2        0        0
  COLON MUCINOUS ADENOCARCINOMA                             2        0        0
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                   0        0        0
  INFILTRATING DUCTAL CARCINOMA                             0        2        0
  INFILTRATING LOBULAR CARCINOMA                            0        1        0
  KIDNEY CLEAR CELL RENAL CARCINOMA                         0        0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        0        1        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        0
  MIXED SEROUS AND ENDOMETRIOID                             0        0        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                         0        0        1
                                                    clus
vv                                                   subtype4 subtype5
  COLON ADENOCARCINOMA                                      0        0
  COLON MUCINOUS ADENOCARCINOMA                             0        0
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                   1        0
  INFILTRATING DUCTAL CARCINOMA                             2        0
  INFILTRATING LOBULAR CARCINOMA                            0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA                         0        4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0
  MIXED SEROUS AND ENDOMETRIOID                             0        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                         0        0
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 subtype7 
       1        1        3 
[1] "subtype7" "subtype7" "subtype7"
D1V11, binary
          cls
clus       0 1
  subtype1 3 1
  subtype2 3 0
  subtype3 0 0
  subtype4 1 1
  subtype5 0 0
  subtype7 2 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    3    0
  subtype3    0    0
  subtype4    1    1
  subtype5    0    0
  subtype7    2    1
   clus
vv  subtype1 subtype2 subtype4 subtype7
  0        3        3        1        2
  2        1        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"
D1V12, binary
          cls
clus       0 1
  subtype1 1 4
  subtype2 0 4
  subtype3 0 3
  subtype4 1 2
  subtype5 0 4
  subtype7 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    4
  subtype2    0    4
  subtype3    0    3
  subtype4    1    2
  subtype5    0    4
  subtype7    0    3
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  BLACK OR AFRICAN AMERICAN        1        0        0        1        0
  WHITE                            4        4        3        2        4
                           clus
vv                          subtype7
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MIRSEQ_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype2 4 0
  subtype3 4 0
  subtype4 3 3
  subtype5 4 0
  subtype6 3 0
subtype2 subtype3 subtype4 subtype5 subtype6 
       4        4        6        4        3 
subtype2 subtype3 subtype4 subtype5 subtype6 
       0        0        3        0        0 
$subtype2
TCGA-44-6147 TCGA-A7-A26E TCGA-A7-A0DB TCGA-A7-A26J 
       27.78        31.36        33.11        20.61 

$subtype3
TCGA-A6-5656 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6781 
       32.91        20.61        20.12        19.66 

$subtype4
TCGA-A7-A13D TCGA-A7-A13E TCGA-BK-A139 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       31.73        20.19        10.16        40.08         7.33         2.66 

$subtype5
TCGA-B2-5635 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
       10.36        32.61        35.90        11.77 

$subtype6
TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A26L 
       34.98        10.22        24.13 

subtype2 subtype3 subtype4 subtype5 subtype6 
   20.61    19.66     2.66    10.36    10.22 
subtype2 subtype3 subtype4 subtype5 subtype6 
   33.11    32.91    40.08    35.90    34.98 
subtype2 subtype3 subtype4 subtype5 subtype6 
  29.570   20.365   15.175   22.190   24.130 
[1] "20.6 - 33.1 (29.6)" "19.7 - 32.9 (20.4)" "2.7 - 40.1 (15.2)" 
[4] "10.4 - 35.9 (22.2)" "10.2 - 35.0 (24.1)"
D2V2, continuous
          vv
clus       BLADDER BREAST COLON ENDOMETRIAL KIDNEY LUNG
  subtype2       0      3     0           0      0    1
  subtype3       0      0     4           0      0    0
  subtype4       3      2     0           1      0    0
  subtype5       0      0     0           0      4    0
  subtype6       0      0     0           3      0    0
D2V3, multiclass
             clus
vv            subtype2 subtype3 subtype4 subtype5 subtype6
  BLADDER            0        0        3        0        0
  BREAST             3        0        2        0        0
  COLON              0        4        0        0        0
  ENDOMETRIAL        0        0        1        0        3
  KIDNEY             0        0        0        4        0
  LUNG               1        0        0        0        0
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  subtype2       0        1        0         2         0         0          1
  subtype3       1        0        0         2         0         0          0
  subtype4       1        0        0         1         1         1          0
  subtype5       3        0        1         0         0         0          0
  subtype6       0        0        0         0         0         0          0
          vv
clus       STAGE IIIC STAGE IV
  subtype2          0        0
  subtype3          1        0
  subtype4          0        1
  subtype5          0        0
  subtype6          0        0
D2V4, multiclass
            clus
vv           subtype2 subtype3 subtype4 subtype5
  STAGE I           0        1        1        3
  STAGE IA          1        0        0        0
  STAGE II          0        0        0        1
  STAGE IIA         2        2        1        0
  STAGE IIB         0        0        1        0
  STAGE III         0        0        1        0
  STAGE IIIA        1        0        0        0
  STAGE IIIC        0        1        0        0
  STAGE IV          0        0        1        0
[1] 9 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
  subtype2  1  2     1
  subtype3  0  1     3
  subtype4  1  2     2
  subtype5  3  1     0
  subtype6  0  0     0
D2V5, multiclass
       clus
vv      subtype2 subtype3 subtype4 subtype5
  T1           1        0        1        3
  T2           2        1        2        1
  T3+T4        1        3        2        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype2  2     1
  subtype3  3     1
  subtype4  2     2
  subtype5  1     0
  subtype6  0     0
D2V6, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       3        4        4        1 
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
       clus
vv      subtype2 subtype3 subtype4
  N0           2        3        2
  N1+N2        1        1        2
[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"
D2V7, binary
          cls
clus       0 1
  subtype2 4 0
  subtype3 1 3
  subtype4 4 2
  subtype5 0 4
  subtype6 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    4    0
  subtype3    1    3
  subtype4    4    2
  subtype5    0    4
  subtype6    3    0
        clus
vv       subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        4        1        4        0        3
  MALE          0        3        2        4        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"
D2V8, binary
          cls
clus       0 1
  subtype2 2 2
  subtype3 4 0
  subtype4 3 1
  subtype5 2 0
  subtype6 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    2
  subtype3    4    0
  subtype4    3    1
  subtype5    2    0
  subtype6    1    2
     clus
vv    subtype2 subtype3 subtype4 subtype5 subtype6
  NO         2        4        3        2        1
  YES        2        0        1        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"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype2                    0                             0
  subtype3                    2                             2
  subtype4                    0                             0
  subtype5                    0                             0
  subtype6                    0                             0
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype2                                       0
  subtype3                                       0
  subtype4                                       1
  subtype5                                       0
  subtype6                                       0
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype2                             2                              1
  subtype3                             0                              0
  subtype4                             2                              0
  subtype5                             0                              0
  subtype6                             0                              0
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 4
  subtype6                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype2                                                  1
  subtype3                                                  0
  subtype4                                                  0
  subtype5                                                  0
  subtype6                                                  0
          vv
clus       MIXED SEROUS AND ENDOMETRIOID
  subtype2                             0
  subtype3                             0
  subtype4                             0
  subtype5                             0
  subtype6                             1
          vv
clus       MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)
  subtype2                                                   0
  subtype3                                                   0
  subtype4                                                   2
  subtype5                                                   0
  subtype6                                                   0
          vv
clus       SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 0
  subtype6                                 2
D2V9, multiclass
                                                     clus
vv                                                    subtype2 subtype3
  COLON ADENOCARCINOMA                                       0        2
  COLON MUCINOUS ADENOCARCINOMA                              0        2
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                    0        0
  INFILTRATING DUCTAL CARCINOMA                              2        0
  INFILTRATING LOBULAR CARCINOMA                             1        0
  KIDNEY CLEAR CELL RENAL CARCINOMA                          0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         1        0
  MIXED SEROUS AND ENDOMETRIOID                              0        0
  MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)        0        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                          0        0
                                                     clus
vv                                                    subtype4 subtype5
  COLON ADENOCARCINOMA                                       0        0
  COLON MUCINOUS ADENOCARCINOMA                              0        0
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                    1        0
  INFILTRATING DUCTAL CARCINOMA                              2        0
  INFILTRATING LOBULAR CARCINOMA                             0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA                          0        4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         0        0
  MIXED SEROUS AND ENDOMETRIOID                              0        0
  MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)        2        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                          0        0
                                                     clus
vv                                                    subtype6
  COLON ADENOCARCINOMA                                       0
  COLON MUCINOUS ADENOCARCINOMA                              0
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                    0
  INFILTRATING DUCTAL CARCINOMA                              0
  INFILTRATING LOBULAR CARCINOMA                             0
  KIDNEY CLEAR CELL RENAL CARCINOMA                          0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         0
  MIXED SEROUS AND ENDOMETRIOID                              1
  MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                          2
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, binary
          cls
clus       0 1
  subtype2 3 0
  subtype3 3 1
  subtype4 3 2
  subtype5 0 0
  subtype6 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    3    0
  subtype3    3    1
  subtype4    3    2
  subtype5    0    0
  subtype6    0    0
   clus
vv  subtype2 subtype3 subtype4
  0        3        3        3
  2        0        1        2
[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"
D2V12, binary
          cls
clus       0 1
  subtype2 0 4
  subtype3 1 3
  subtype4 1 5
  subtype5 0 4
  subtype6 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    0    4
  subtype3    1    3
  subtype4    1    5
  subtype5    0    4
  subtype6    1    2
                           clus
vv                          subtype2 subtype3 subtype4 subtype5 subtype6
  BLACK OR AFRICAN AMERICAN        0        1        1        0        1
  WHITE                            4        3        5        4        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MIRSEQ_MATURE_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 6 0
  subtype2 7 2
  subtype3 7 1
subtype1 subtype2 subtype3 
       6        9        8 
subtype1 subtype2 subtype3 
       0        2        1 
$subtype1
TCGA-44-6146 TCGA-44-6147 TCGA-B2-5635 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
        9.93        27.78        10.36        32.61        35.90        11.77 

$subtype2
TCGA-A7-A26E TCGA-44-6775 TCGA-A6-6781 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       31.36        23.18        19.66        33.11        31.73        20.19 
TCGA-A7-A26J TCGA-BK-A26L TCGA-BL-A13J 
       20.61        24.13         2.66 

$subtype3
TCGA-A6-5656 TCGA-A6-6650 TCGA-A6-6780 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 
       32.91        20.61        20.12        34.98        10.22        10.16 
TCGA-BL-A0C8 TCGA-BL-A13I 
       40.08         7.33 

subtype1 subtype2 subtype3 
    9.93     2.66     7.33 
subtype1 subtype2 subtype3 
   35.90    33.11    40.08 
subtype1 subtype2 subtype3 
  19.775   23.180   20.365 
[1] "9.9 - 35.9 (19.8)" "2.7 - 33.1 (23.2)" "7.3 - 40.1 (20.4)"
D3V2, continuous
          vv
clus       BLADDER BREAST COLON ENDOMETRIAL KIDNEY LUNG
  subtype1       0      0     0           0      4    2
  subtype2       1      5     1           1      0    1
  subtype3       2      0     3           3      0    0
D3V3, multiclass
             clus
vv            subtype1 subtype2 subtype3
  BLADDER            0        1        2
  BREAST             0        5        0
  COLON              0        1        3
  ENDOMETRIAL        0        1        3
  KIDNEY             4        0        0
  LUNG               2        1        0
[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       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        1        0        1         0         1         0
  subtype2       0        0        1        0         3         1         0
  subtype3       2        0        0        0         2         0         1
          vv
clus       STAGE IIIA STAGE IIIC STAGE IV
  subtype1          0          0        0
  subtype2          1          1        1
  subtype3          0          0        0
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        2
  STAGE IA          1        0        0
  STAGE IB          0        1        0
  STAGE II          1        0        0
  STAGE IIA         0        3        2
  STAGE IIB         1        1        0
  STAGE III         0        0        1
  STAGE IIIA        0        1        0
  STAGE IIIC        0        1        0
  STAGE IV          0        1        0
[1] 10  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  1     1
  subtype2  0  5     3
  subtype3  1  1     3
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           4        0        1
  T2           1        5        1
  T3+T4        1        3        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  2     0
  subtype2  4     4
  subtype3  4     0
D3V6, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        8        4 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
       clus
vv      subtype2 subtype3
  N0           4        4
  N1+N2        4        0
[1] 2 2
[1] FALSE
D3V7, binary
          cls
clus       0 1
  subtype1 1 5
  subtype2 7 2
  subtype3 5 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype2    7    2
  subtype3    5    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        7        5
  MALE          5        2        3
[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"
D3V8, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 4 4
  subtype3 6 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    4    4
  subtype3    6    1
     clus
vv    subtype1 subtype2 subtype3
  NO         4        4        6
  YES        0        4        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"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                    0                             0
  subtype2                    0                             1
  subtype3                    2                             1
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                             0                              0
  subtype2                             4                              1
  subtype3                             0                              0
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                 4
  subtype2                                 0
  subtype3                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                  1
  subtype2                                                  1
  subtype3                                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID
  subtype1                            1                             0
  subtype2                            0                             0
  subtype3                            0                             1
          vv
clus       MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)
  subtype1                                                   0
  subtype2                                                   1
  subtype3                                                   1
          vv
clus       SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                                 0
  subtype2                                 1
  subtype3                                 1
D3V9, multiclass
                                                     clus
vv                                                    subtype1 subtype2
  COLON ADENOCARCINOMA                                       0        0
  COLON MUCINOUS ADENOCARCINOMA                              0        1
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                    0        0
  INFILTRATING DUCTAL CARCINOMA                              0        4
  INFILTRATING LOBULAR CARCINOMA                             0        1
  KIDNEY CLEAR CELL RENAL CARCINOMA                          4        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         1        1
  LUNG MUCINOUS ADENOCARCINOMA                               1        0
  MIXED SEROUS AND ENDOMETRIOID                              0        0
  MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)        0        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                          0        1
                                                     clus
vv                                                    subtype3
  COLON ADENOCARCINOMA                                       2
  COLON MUCINOUS ADENOCARCINOMA                              1
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                    1
  INFILTRATING DUCTAL CARCINOMA                              0
  INFILTRATING LOBULAR CARCINOMA                             0
  KIDNEY CLEAR CELL RENAL CARCINOMA                          0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         0
  LUNG MUCINOUS ADENOCARCINOMA                               0
  MIXED SEROUS AND ENDOMETRIOID                              1
  MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                          1
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        2        2 
character(0)
D3V11, binary
          cls
clus       0 1
  subtype1 0 0
  subtype2 4 3
  subtype3 5 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    0
  subtype2    4    3
  subtype3    5    0
   clus
vv  subtype2 subtype3
  0        4        5
  2        3        0
[1] 2 2
[1] FALSE
D3V12, binary
          cls
clus       0 1
  subtype1 0 6
  subtype2 1 8
  subtype3 2 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    1    8
  subtype3    2    6
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        1        2
  WHITE                            6        8        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 5 0
  subtype2 6 0
  subtype3 2 1
  subtype4 2 1
  subtype5 4 0
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        6        3        3        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        0        1        1        0 
$subtype1
TCGA-44-6146 TCGA-A6-5656 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6781 
        9.93        32.91        20.61        20.12        19.66 

$subtype2
TCGA-44-6147 TCGA-A7-A26E TCGA-44-6775 TCGA-A7-A0DB TCGA-A7-A26J TCGA-BK-A0CA 
       27.78        31.36        23.18        33.11        20.61        34.98 

$subtype3
TCGA-A7-A13D TCGA-BL-A0C8 TCGA-BL-A13J 
       31.73        40.08         2.66 

$subtype4
TCGA-A7-A13E TCGA-BK-A0CC TCGA-BK-A26L 
       20.19        10.22        24.13 

$subtype5
TCGA-B2-5635 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
       10.36        32.61        35.90        11.77 

subtype1 subtype2 subtype3 subtype4 subtype5 
    9.93    20.61     2.66    10.22    10.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
   32.91    34.98    40.08    24.13    35.90 
subtype1 subtype2 subtype3 subtype4 subtype5 
   20.12    29.57    31.73    20.19    22.19 
[1] "9.9 - 32.9 (20.1)"  "20.6 - 35.0 (29.6)" "2.7 - 40.1 (31.7)" 
[4] "10.2 - 24.1 (20.2)" "10.4 - 35.9 (22.2)"
D4V2, continuous
          vv
clus       BLADDER BREAST COLON ENDOMETRIAL KIDNEY LUNG
  subtype1       0      0     4           0      0    1
  subtype2       0      3     0           1      0    2
  subtype3       2      1     0           0      0    0
  subtype4       0      1     0           2      0    0
  subtype5       0      0     0           0      4    0
D4V3, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  BLADDER            0        0        2        0        0
  BREAST             0        3        1        1        0
  COLON              4        0        0        0        0
  ENDOMETRIAL        0        1        0        2        0
  KIDNEY             0        0        0        0        4
  LUNG               1        2        0        0        0
[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       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1        0        0        0         2         1          0
  subtype2       0        1        1        0         2         0          1
  subtype3       1        0        0        0         1         0          0
  subtype4       0        0        0        0         0         1          0
  subtype5       3        0        0        1         0         0          0
          vv
clus       STAGE IIIC STAGE IV
  subtype1          1        0
  subtype2          0        0
  subtype3          0        1
  subtype4          0        0
  subtype5          0        0
D4V4, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        5        3        1        4 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[13] "subtype5" "subtype5" "subtype5" "subtype3" "subtype3"
            clus
vv           subtype1 subtype2 subtype3 subtype5
  STAGE I           1        0        1        3
  STAGE IA          0        1        0        0
  STAGE IB          0        1        0        0
  STAGE II          0        0        0        1
  STAGE IIA         2        2        1        0
  STAGE IIB         1        0        0        0
  STAGE IIIA        0        1        0        0
  STAGE IIIC        1        0        0        0
  STAGE IV          0        0        1        0
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  0  1     4
  subtype2  1  3     1
  subtype3  1  1     1
  subtype4  0  1     0
  subtype5  3  1     0
D4V5, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        5        3        1        4 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[13] "subtype5" "subtype5" "subtype5" "subtype3" "subtype3"
       clus
vv      subtype1 subtype2 subtype3 subtype5
  T1           0        1        1        3
  T2           1        3        1        1
  T3+T4        4        1        1        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  4     1
  subtype2  3     1
  subtype3  1     1
  subtype4  0     1
  subtype5  1     0
D4V6, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
[4] "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        4        2        1        1 
[1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[8] "subtype2" "subtype2"
       clus
vv      subtype1 subtype2
  N0           4        3
  N1+N2        1        1
[1] 2 2
[1] FALSE
D4V7, binary
          cls
clus       0 1
  subtype1 1 4
  subtype2 6 0
  subtype3 1 2
  subtype4 3 0
  subtype5 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    4
  subtype2    6    0
  subtype3    1    2
  subtype4    3    0
  subtype5    0    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1        6        1        3        0
  MALE          4        0        2        0        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus       0 1
  subtype1 5 0
  subtype2 4 2
  subtype3 1 1
  subtype4 1 2
  subtype5 2 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    4    2
  subtype3    1    1
  subtype4    1    2
  subtype5    2    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         5        4        1        1        2
  YES        0        2        1        2        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"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                    2                             2
  subtype2                    0                             0
  subtype3                    0                             0
  subtype4                    0                             0
  subtype5                    0                             0
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                             0                              0
  subtype2                             2                              1
  subtype3                             1                              0
  subtype4                             1                              0
  subtype5                             0                              0
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                 0
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 4
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                  0
  subtype2                                                  2
  subtype3                                                  0
  subtype4                                                  0
  subtype5                                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID
  subtype1                            1                             0
  subtype2                            0                             1
  subtype3                            0                             0
  subtype4                            0                             0
  subtype5                            0                             0
          vv
clus       MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE)
  subtype1                                                   0
  subtype2                                                   0
  subtype3                                                   1
  subtype4                                                   0
  subtype5                                                   0
          vv
clus       SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                                 0
  subtype2                                 0
  subtype3                                 0
  subtype4                                 2
  subtype5                                 0
D4V9, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        6        2        3        4 
 [1] "subtype1" "subtype2" "subtype2" "subtype5" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype5" "subtype5" "subtype5" "subtype2" "subtype4" "subtype4"
                                                    clus
vv                                                   subtype1 subtype2 subtype4
  COLON ADENOCARCINOMA                                      2        0        0
  COLON MUCINOUS ADENOCARCINOMA                             2        0        0
  INFILTRATING DUCTAL CARCINOMA                             0        2        1
  INFILTRATING LOBULAR CARCINOMA                            0        1        0
  KIDNEY CLEAR CELL RENAL CARCINOMA                         0        0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        0        2        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        0
  MIXED SEROUS AND ENDOMETRIOID                             0        1        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                         0        0        2
                                                    clus
vv                                                   subtype5
  COLON ADENOCARCINOMA                                      0
  COLON MUCINOUS ADENOCARCINOMA                             0
  INFILTRATING DUCTAL CARCINOMA                             0
  INFILTRATING LOBULAR CARCINOMA                            0
  KIDNEY CLEAR CELL RENAL CARCINOMA                         4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        0
  LUNG MUCINOUS ADENOCARCINOMA                              0
  MIXED SEROUS AND ENDOMETRIOID                             0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                         0
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        1        2 
character(0)
D4V11, binary
          cls
clus       0 1
  subtype1 3 1
  subtype2 3 0
  subtype3 2 1
  subtype4 0 1
  subtype5 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    3    0
  subtype3    2    1
  subtype4    0    1
  subtype5    0    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        3        3        2        0
  2        1        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"
D4V12, binary
          cls
clus       0 1
  subtype1 1 4
  subtype2 0 6
  subtype3 1 2
  subtype4 1 2
  subtype5 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    4
  subtype2    0    6
  subtype3    1    2
  subtype4    1    2
  subtype5    0    4
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  BLACK OR AFRICAN AMERICAN        1        0        1        1        0
  WHITE                            4        6        2        2        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
