[1] "ofn"        "-oTCESC-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/CESC-TP/22489370/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/22541064/CESC-TP.mergedcluster.txt"

nPatients in clinical file=307, in cluster file=307, common to both=307
[1]  10 307
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
 15 112  56  59  53 
  1   2   3   4   5 
 15 112  56  59  53 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 72 122 113 
  1   2   3 
 72 122 113 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
60 45 68 
 1  2  3 
60 45 68 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
32 49 51 23 18 
 1  2  3  4  5 
32 49 51 23 18 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
 61 103  69  71 
  1   2   3   4 
 61 103  69  71 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 72 195  37 
  1   2   3 
 72 195  37 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
108  78 121 
  1   2   3 
108  78 121 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 60 102  74  26  45 
  1   2   3   4   5 
 60 102  74  26  45 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
104  82 108 
  1   2   3 
104  82 108 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 29  81 109  42  33 
  1   2   3   4   5 
 29  81 109  42  33 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                          
 [2] "VITAL_STATUS"                            
 [3] "DAYS_TO_DEATH"                           
 [4] "DAYS_TO_LAST_FOLLOWUP"                   
 [5] "TUMOR_TISSUE_SITE"                       
 [6] "PATHOLOGIC_STAGE"                        
 [7] "PATHOLOGY_T_STAGE"                       
 [8] "PATHOLOGY_N_STAGE"                       
 [9] "PATHOLOGY_M_STAGE"                       
[10] "GENDER"                                  
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"    
[12] "RADIATION_THERAPY"                       
[13] "HISTOLOGICAL_TYPE"                       
[14] "NUMBER_PACK_YEARS_SMOKED"                
[15] "NUMBER_OF_LYMPH_NODES"                   
[16] "RACE"                                    
[17] "ETHNICITY"                               
[18] "WEIGHT_KG_AT_DIAGNOSIS"                  
[19] "TUMOR_STATUS"                            
[20] "NEOPLASM_HISTOLOGIC_GRADE"               
[21] "TOBACCO_SMOKING_YEAR_STOPPED"            
[22] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"       
[23] "TOBACCO_SMOKING_HISTORY"                 
[24] "AGEBEGANSMOKINGINYEARS"                  
[25] "RADIATION_THERAPY_STATUS"                
[26] "PREGNANCIES_COUNT_TOTAL"                 
[27] "PREGNANCIES_COUNT_STILLBIRTH"            
[28] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"    
[29] "PREGNANCIES_COUNT_LIVE_BIRTH"            
[30] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"    
[31] "PREGNANCIES_COUNT_ECTOPIC"               
[32] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT"
[33] "LYMPH_NODE_LOCATION"                     
[34] "POS_LYMPH_NODE_LOCATION"                 
[35] "MENOPAUSE_STATUS"                        
[36] "LYMPHOVASCULAR_INVOLVEMENT"              
[37] "LYMPH_NODES_EXAMINED_HE_COUNT"           
[38] "LYMPH_NODES_EXAMINED"                    
[39] "KERATINIZATION_SQUAMOUS_CELL"            
[40] "INITIAL_PATHOLOGIC_DX_YEAR"              
[41] "HYSTERECTOMY_TYPE"                       
[42] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"     
[43] "HEIGHT_CM_AT_DIAGNOSIS"                  
[44] "CORPUS_INVOLVEMENT"                      
[45] "CHEMO_CONCURRENT_TYPE"                   
[46] "CERVIX_SUV_RESULTS"                      
[47] "CAUSE_OF_DEATH"                          
[48] "AGE_AT_DIAGNOSIS"                        
[49] "CLINICAL_STAGE"                          

Input Data has 49 rows and 307 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=206,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'PREGNANCY_SPONTANEOUS_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 29:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'PREGNANCY_THERAPEUTIC_ABORTION_COUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 31:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 32:'CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              BILATERAL PELVIC WALL INVOLVEMENT ON IMAGING
freq.values   "1"                                         
freq.contrast "10"                                        
both >= 3     "FALSE"                                     
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "10"                                                                                                                               
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NEGATIVE NO EXTENSION NO PELVIC SPREAD
freq.values   "1"                       "2"      "1"          "1"             
freq.contrast "10"                      "9"      "10"         "10"            
both >= 3     "FALSE"                   "FALSE"  "FALSE"      "FALSE"         
              PELVIC SPREAD
freq.values   "1"          
freq.contrast "10"         
both >= 3     "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "10"                                                                        
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "10"                                                                                                                                      
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "10"                                                                     
both >= 3     "FALSE"                                                                  
Variable 33:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 34:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 35:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 36:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 37:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 40:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 41:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'CAUSE_OF_DEATH':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARDIOPULMONARY ARREST LUNG CANCER RENAL FAILURE
freq.values   "1"                    "1"         "1"          
freq.contrast "2"                    "2"         "2"          
both >= 3     "FALSE"                "FALSE"     "FALSE"      
Variable 48:'AGE_AT_DIAGNOSIS':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'CLINICAL_STAGE':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=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 307 columns, 1 survival variables, and 38 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                      
 [2] "PATHOLOGY_T_STAGE"                   
 [3] "PATHOLOGY_N_STAGE"                   
 [4] "PATHOLOGY_M_STAGE"                   
 [5] "RADIATION_THERAPY"                   
 [6] "HISTOLOGICAL_TYPE"                   
 [7] "NUMBER_PACK_YEARS_SMOKED"            
 [8] "NUMBER_OF_LYMPH_NODES"               
 [9] "RACE"                                
[10] "ETHNICITY"                           
[11] "WEIGHT_KG_AT_DIAGNOSIS"              
[12] "TUMOR_STATUS"                        
[13] "NEOPLASM_HISTOLOGIC_GRADE"           
[14] "TOBACCO_SMOKING_YEAR_STOPPED"        
[15] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"   
[16] "TOBACCO_SMOKING_HISTORY"             
[17] "AGEBEGANSMOKINGINYEARS"              
[18] "RADIATION_THERAPY_STATUS"            
[19] "PREGNANCIES_COUNT_TOTAL"             
[20] "PREGNANCIES_COUNT_STILLBIRTH"        
[21] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"
[22] "PREGNANCIES_COUNT_LIVE_BIRTH"        
[23] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"
[24] "PREGNANCIES_COUNT_ECTOPIC"           
[25] "POS_LYMPH_NODE_LOCATION"             
[26] "MENOPAUSE_STATUS"                    
[27] "LYMPHOVASCULAR_INVOLVEMENT"          
[28] "LYMPH_NODES_EXAMINED_HE_COUNT"       
[29] "LYMPH_NODES_EXAMINED"                
[30] "KERATINIZATION_SQUAMOUS_CELL"        
[31] "INITIAL_PATHOLOGIC_DX_YEAR"          
[32] "HISTORY_HORMONAL_CONTRACEPTIVES_USE" 
[33] "HEIGHT_CM_AT_DIAGNOSIS"              
[34] "CORPUS_INVOLVEMENT"                  
[35] "CHEMO_CONCURRENT_TYPE"               
[36] "CERVIX_SUV_RESULTS"                  
[37] "AGE_AT_DIAGNOSIS"                    
[38] "CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
141  72  21  10 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
141  72  21  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
141  72  21  10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
141  72  21  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=11, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=74, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=22, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=TRUE
AGEBEGANSMOKINGINYEARS, nv=28, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=15, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PREGNANCY_SPONTANEOUS_ABORTION_COUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PREGNANCY_THERAPEUTIC_ABORTION_COUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=11, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=49, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=37, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=17, binary=FALSE, numeric=TRUE
AGE_AT_DIAGNOSIS, nv=62, binary=FALSE, numeric=TRUE
CLINICAL_STAGE, nv=17, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 13  1
  subtype2 79 29
  subtype3 42 11
  subtype4 43 15
  subtype5 37 12
subtype1 subtype2 subtype3 subtype4 subtype5 
      14      108       53       58       49 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1       29       11       15       12 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1BI TCGA-C5-A7CJ TCGA-C5-A8ZZ TCGA-EA-A3HS TCGA-EK-A2R8 
       17.52        36.56       101.82        20.91        31.53         1.45 
TCGA-EK-A2RE TCGA-EX-A8YF TCGA-FU-A3YQ TCGA-JW-A5VI TCGA-MA-AA42 TCGA-VS-A958 
        1.87        15.55        28.31        24.56         8.52        50.14 
TCGA-VS-A9UA TCGA-VS-A9UB 
       28.50        29.95 

$subtype2
TCGA-EK-A2GZ TCGA-VS-A9V4 TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       12.59         4.34        17.82        57.04        23.67        11.44 
TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1ML 
      144.16         5.46        31.40        57.73        35.61        20.91 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HE 
       40.93        73.18        73.45        78.35        52.01        18.02 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      154.32       134.33        20.35       147.35        17.19       155.77 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR 
        9.34        13.61         2.73        45.83        99.91        27.52 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VL 
       14.73         1.12        95.11        63.98        87.75        55.63 
TCGA-DS-A0VM TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3Y4 
      117.99         8.28        40.87        30.90        13.05        36.89 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF 
       31.73        26.01        12.13        14.89        25.91        27.22 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       60.72        26.27         6.64         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GN TCGA-EX-A3L1 
        0.89        40.96         1.74         1.64         0.89        15.22 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC 
       23.84        20.98        14.01        10.55        17.75        16.57 
TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AU 
       21.67        78.71        29.85        20.48         8.28        11.28 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA 
        0.89         0.82        22.52        11.38        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD 
       15.58        15.95         9.04        22.62        19.59        11.67 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94X 
       10.03        46.52        23.97        19.96        59.18        16.64 
TCGA-VS-A94Y TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UC TCGA-VS-A9UD 
        4.73        51.32        50.47        43.40        27.12        24.30 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UY 
       45.11        14.53        47.87        47.47        15.85        18.25 
TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       18.84        18.25        26.01        67.59        19.13         1.41 

$subtype3
TCGA-BI-A0VR TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LX TCGA-C5-A2LZ 
       49.48        38.99         2.43         3.58        83.05       100.14 
TCGA-C5-A7CG TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A8XI TCGA-DG-A2KK TCGA-DG-A2KL 
      210.67        15.48       131.11         8.35        82.06        44.94 
TCGA-DS-A3LQ TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R 
       22.98        31.36        24.56        27.29        27.25        13.48 
TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A69L 
        0.36         1.51         0.43         2.33        20.35        19.79 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       20.78        14.93        36.36        18.15       209.59        20.91 
TCGA-MA-AA3X TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-UC-A7PF TCGA-UC-A7PG 
       20.28        35.05        16.41        17.56        93.99        12.16 
TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z 
       32.42        32.15        11.51        31.27        40.87        33.37 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A9UH TCGA-VS-A9UU 
       40.14        15.68        56.35        55.50        46.92        14.53 
TCGA-VS-A9UV TCGA-VS-A9V3 TCGA-XS-A8TJ TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        3.42        17.75        29.26         0.16         3.91 

$subtype4
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1BQ 
       14.70         8.32         1.48        68.84       177.04        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       67.46        46.32        35.01        44.22        38.43        33.24 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A8YT TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A1QS 
       17.85        20.42        20.81        58.88        16.18        39.55 
TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EX-A1H6 
       26.40        24.82        26.79        47.77         0.07         7.92 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A57G TCGA-FU-A770 
       12.23        19.04        16.11        36.26        35.44         1.12 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VG 
        9.44       137.16        66.81        96.95        81.96        27.42 
TCGA-JW-A5VH TCGA-JW-A5VL TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA3Z 
        3.29        15.58         0.30        13.35        17.82        19.56 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73R 
       19.96        54.81        20.84        16.14        14.07        18.64 
TCGA-UC-A7PI TCGA-VS-A8EL TCGA-VS-A952 TCGA-VS-A9U7 TCGA-VS-A9UJ TCGA-VS-A9UQ 
       69.50        65.49        58.45        48.39         1.71        41.52 
TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V5 TCGA-VS-AA62 
       26.07        67.20        16.24        15.42 

$subtype5
TCGA-C5-A8XJ TCGA-ZJ-AAX4 TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M8 
      146.86         0.69        18.74       173.29        82.85        30.21 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-DS-A0VK 
       53.16         0.46        94.95        50.99        23.51        36.76 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A3HQ TCGA-EA-A3QE TCGA-EA-A50E 
      118.65        16.83        17.52        37.35        25.02         7.46 
TCGA-EA-A6QX TCGA-EK-A2PI TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       24.00        19.27         0.13         0.30         4.24         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HG-A2PA 
        0.10         0.49        31.36        26.14        16.14        25.41 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q8 
      147.39       129.37        21.44        28.37        21.11        44.61 
TCGA-LP-A4AX TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-Q1-A73P TCGA-Q1-A73Q 
       12.49         9.17        28.08        34.62        15.88         9.34 
TCGA-RA-A741 TCGA-VS-A8EG TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A9UM 
       14.60        45.57        53.59        36.13        39.78        27.25 
TCGA-VS-A9V1 
        5.16 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.45     0.39     0.16     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  101.82   155.77   210.67   177.04   173.29 
subtype1 subtype2 subtype3 subtype4 subtype5 
  26.435   20.695   22.980   22.830   25.020 
[1] "1.4 - 101.8 (26.4)" "0.4 - 155.8 (20.7)" "0.2 - 210.7 (23.0)"
[4] "0.1 - 177.0 (22.8)" "0.1 - 173.3 (25.0)"
D1V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1  3  8  2  0
  subtype2 50 25  6  2
  subtype3 21 12  8  4
  subtype4 32 17  2  1
  subtype5 29  8  3  1
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3       50       21       32       29
  T2        8       25       12       17        8
  T3        2        6        8        2        3
  T4        0        2        4        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"
D1V4, binary
          cls
clus        0  1
  subtype1  7  3
  subtype2 42 22
  subtype3 19 13
  subtype4 34  9
  subtype5 27  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    3
  subtype2   42   22
  subtype3   19   13
  subtype4   34    9
  subtype5   27    9
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        7       42       19       34       27
  1        3       22       13        9        9
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 42  4
  subtype3 22  1
  subtype4 22  4
  subtype5 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   42    4
  subtype3   22    1
  subtype4   22    4
  subtype5   17    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        5       42       22       22       17
  1        0        4        1        4        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"
D1V6, binary
          cls
clus        0  1
  subtype1  1  8
  subtype2 15 52
  subtype3  8 31
  subtype4 17 19
  subtype5 12 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    8
  subtype2   15   52
  subtype3    8   31
  subtype4   17   19
  subtype5   12   15
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1       15        8       17       12
  YES        8       52       31       19       15
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             1                               14
  subtype2             3                               96
  subtype3             0                               56
  subtype4             2                               31
  subtype5             0                               45
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             0
  subtype2                                             2
  subtype3                                             0
  subtype4                                             4
  subtype5                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   0
  subtype2                                   3
  subtype3                                   0
  subtype4                                  13
  subtype5                                   5
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         1
  subtype3                                         0
  subtype4                                         2
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            0
  subtype2                                            7
  subtype3                                            0
  subtype4                                            7
  subtype5                                            3
D1V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        1        3        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    14       96       56
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        3        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        1        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        7        0
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    31       45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 13        5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         7        3
[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"
D1V8, continuous
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         0
  subtype2                                1     7                        11
  subtype3                                0     4                         9
  subtype4                                4     3                         4
  subtype5                                2     5                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    13
  subtype2                                         1    82
  subtype3                                         0    29
  subtype4                                         0    42
  subtype5                                         1    36
D1V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        0        4
  ASIAN                                            0        7        4        3
  BLACK OR AFRICAN AMERICAN                        0       11        9        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0        0
  WHITE                                           13       82       29       42
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 2
  ASIAN                                            5
  BLACK OR AFRICAN AMERICAN                        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           36
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
          cls
clus        0  1
  subtype1  2  9
  subtype2  7 63
  subtype3  2 28
  subtype4  9 31
  subtype5  3 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    9
  subtype2    7   63
  subtype3    2   28
  subtype4    9   31
  subtype5    3   32
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        7        2        9        3
  NOT HISPANIC OR LATINO        9       63       28       31       32
[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"
D1V12, continuous
D1V13, binary
          cls
clus        0  1
  subtype1 11  3
  subtype2 71 31
  subtype3 34 14
  subtype4 42 14
  subtype5 35 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    3
  subtype2   71   31
  subtype3   34   14
  subtype4   42   14
  subtype5   35   14
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       11       71       34       42       35
  WITH TUMOR        3       31       14       14       14
[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       G1 G2 G3 G4 GX
  subtype1  2  6  7  0  0
  subtype2  2 40 56  1  9
  subtype3  4 25 22  0  5
  subtype4  8 30 16  0  5
  subtype5  2 28 14  0  5
D1V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        2        2        4        8        2
  G2        6       40       25       30       28
  G3        7       56       22       16       14
  G4        0        1        0        0        0
  GX        0        9        5        5        5
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2       18        9        7        7 
 [1] "subtype4" "subtype4" "subtype2" "subtype5" "subtype3" "subtype2"
 [7] "subtype5" "subtype4" "subtype2" "subtype5" "subtype3" "subtype4"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype4" "subtype5" "subtype3" "subtype3"
[25] "subtype5" "subtype4" "subtype2" "subtype3" "subtype2" "subtype5"
[31] "subtype4" "subtype3" "subtype2" "subtype5" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D1V16, continuous
D1V17, continuous
D1V18, continuous
D1V19, binary
          cls
clus        0  1
  subtype1  1  0
  subtype2 10  2
  subtype3  4  1
  subtype4  5  0
  subtype5  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    0
  subtype2   10    2
  subtype3    4    1
  subtype4    5    0
  subtype5    5    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  COMPLETED AS PLANNED           1       10        4        5        5
  TREATMENT NOT COMPLETED        0        2        1        0        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"
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   1
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       1
  subtype2                                   4                      11
  subtype3                                   1                       8
  subtype4                                   2                       9
  subtype5                                   0                       7
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       0
  subtype2                       0                       1
  subtype3                       0                       3
  subtype4                       0                       1
  subtype5                       1                       5
D1V26, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2       16       12       13       13 
 [1] "subtype4" "subtype5" "subtype2" "subtype2" "subtype4" "subtype4"
 [7] "subtype5" "subtype4" "subtype4" "subtype5" "subtype4" "subtype2"
[13] "subtype5" "subtype5" "subtype3" "subtype4" "subtype2" "subtype2"
[19] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype2"
[25] "subtype5" "subtype2" "subtype5" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype4" "subtype5" "subtype2" "subtype2" "subtype5"
[37] "subtype3" "subtype5" "subtype5" "subtype3" "subtype3" "subtype3"
[43] "subtype4" "subtype3" "subtype2" "subtype4" "subtype2" "subtype5"
[49] "subtype4" "subtype2" "subtype5" "subtype2" "subtype2" "subtype3"
                                     clus
vv                                    subtype2 subtype3 subtype4 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        4        1        2        0
  OTHER LOCATION, SPECIFY                   11        8        9        7
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    1        3        1        5
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             0
  subtype4                                             1
  subtype5                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              0
  subtype2                                             11
  subtype3                                              4
  subtype4                                              5
  subtype5                                              5
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 3
  subtype2                                                                                24
  subtype3                                                                                25
  subtype4                                                                                19
  subtype5                                                                                11
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           10
  subtype2                                                                                           46
  subtype3                                                                                           17
  subtype4                                                                                           28
  subtype5                                                                                           20
D1V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       10
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       46
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       17
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       28
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       20
[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"
D1V28, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2 25 23
  subtype3 12 15
  subtype4 23 14
  subtype5  9 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2   25   23
  subtype3   12   15
  subtype4   23   14
  subtype5    9   19
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT         2       25       12       23        9
  PRESENT        3       23       15       14       19
[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"
D1V29, continuous
D1V30, continuous
D1V31, binary
          cls
clus        0  1
  subtype1  5  6
  subtype2 16 50
  subtype3 12 21
  subtype4  8 18
  subtype5  8 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    6
  subtype2   16   50
  subtype3   12   21
  subtype4    8   18
  subtype5    8   22
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            5       16       12        8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        6       50       21       18
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA            8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       22
[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"
D1V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           4          4
  subtype2            5          18         33
  subtype3            1          10         17
  subtype4            6          12         20
  subtype5            3          10         11
D1V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        0        5        1        6        3
  FORMER USER         4       18       10       12       10
  NEVER USED          4       33       17       20       11
[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"
D1V34, continuous
D1V35, binary
          cls
clus        0  1
  subtype1  3  1
  subtype2 30  6
  subtype3 15  2
  subtype4 25  5
  subtype5 19  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2   30    6
  subtype3   15    2
  subtype4   25    5
  subtype5   19    4
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT         3       30       15       25       19
  PRESENT        1        6        2        5        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         8     0
  subtype2           1        45     1
  subtype3           1        21     0
  subtype4           3        16     0
  subtype5           0        10     1
D1V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        0        1        1        3        0
  CISPLATIN          8       45       21       16       10
  OTHER              0        1        0        0        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        7        4        3        2 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype4"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype4" "subtype4"
[13] "subtype2" "subtype3"
D1V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       0        0         0         0        1         2         2
  subtype2       2        1         0         0       16        23        14
  subtype3       1        0         0         1        3        14         3
  subtype4       1        0         0         0        5        17        13
  subtype5       1        0         1         0        9        21         5
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         2          0          0         5         0
  subtype2        1         3          4          2        22         0
  subtype3        0         1          0          1         7         1
  subtype4        1         2          0          3         7         0
  subtype5        2         0          1          1         3         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          1          2         0         0
  subtype2          1         15         2         3
  subtype3          1         15         4         2
  subtype4          0          6         0         4
  subtype5          0          4         1         3
D1V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        2        1        1        1
  STAGE IA          0        1        0        0        0
  STAGE IA1         0        0        0        0        1
  STAGE IA2         0        0        1        0        0
  STAGE IB          1       16        3        5        9
  STAGE IB1         2       23       14       17       21
  STAGE IB2         2       14        3       13        5
  STAGE II          0        1        0        1        2
  STAGE IIA         2        3        1        2        0
  STAGE IIA1        0        4        0        0        1
  STAGE IIA2        0        2        1        3        1
  STAGE IIB         5       22        7        7        3
  STAGE III         0        0        1        0        0
  STAGE IIIA        1        1        1        0        0
  STAGE IIIB        2       15       15        6        4
  STAGE IVA         0        2        4        0        1
  STAGE IVB         0        3        2        4        3
[1] 17  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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 53 17
  subtype2 87 30
  subtype3 82 25
subtype1 subtype2 subtype3 
      70      117      107 
subtype1 subtype2 subtype3 
      17       30       25 
$subtype1
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
      146.86        14.70        17.52        31.40        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2M1 
       53.16        35.61         0.46        20.91        44.22        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8XI 
       33.24        18.02        17.85        20.35         2.73         8.35 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A439 
        1.12        95.11        82.06        16.18        17.52        31.73 
TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RL 
       26.79        27.25        27.22         0.89         0.13        47.77 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A3EO 
        1.64         0.49        20.35         7.92        12.23        16.11 
TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       14.01         1.12       147.39       137.16        66.81        96.95 
TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-LP-A7HU 
       81.96         3.29        28.37        44.61         0.30        13.35 
TCGA-MA-AA43 TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P 
       11.38        54.81         2.96        15.58        16.14        15.88 
TCGA-Q1-A73R TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       18.64        69.50        19.96        36.13        39.78        58.45 
TCGA-VS-A957 TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       55.50         1.71        14.53        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V5 
       26.07        67.20         5.16        16.24 

$subtype2
TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-C5-A1BE TCGA-C5-A1BL TCGA-C5-A1BQ 
        8.32         0.69        17.82        68.84       173.29        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
       67.46        30.21        40.93        73.45        83.05       100.14 
TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
       52.01       210.67       154.32       134.33        15.48       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8YQ TCGA-C5-A8ZZ 
      155.77       131.11        94.95        13.61        23.51        20.91 
TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-DG-A2KL TCGA-DS-A0VK TCGA-DS-A0VL 
       17.03         4.90       160.41        44.94        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A1QT 
      117.99        28.90        28.31        22.98        16.83        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A50E 
       37.35        30.90        31.53        13.05        12.13         7.46 
TCGA-EA-A5O9 TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR 
       25.91        24.00         0.36        60.72         6.64       113.16 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        1.51        19.27         0.43        40.96         0.30         4.24 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.07         1.87         0.43         2.33         0.07         0.10 
TCGA-EK-A3GN TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        0.89        19.04        31.36        20.98        26.14        16.14 
TCGA-FU-A5XV TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VI 
       10.55        20.78        14.93       129.37        29.85        24.56 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       20.48        15.58         8.28        18.15       209.59        20.91 
TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI 
        0.82        20.28        19.56         9.17         8.52        34.62 
TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       19.96        20.84        16.41        15.95         9.04        17.56 
TCGA-Q1-A73Q TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
        9.34        12.16        10.03        46.52        45.57        32.42 
TCGA-VS-A8EK TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A950 TCGA-VS-A953 
       27.25        53.59        11.51        59.18        40.14        15.68 
TCGA-VS-A954 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI 
       56.35        50.47        48.39        27.12        24.30        45.11 
TCGA-VS-A9UM TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 
       27.25         3.42        18.25        18.25        17.75        26.01 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       19.13         1.41         0.16 

$subtype3
TCGA-DS-A1OC TCGA-EK-A2GZ TCGA-FU-A3TX TCGA-VS-A9V4 TCGA-BI-A0VR TCGA-BI-A0VS 
       12.36        12.59         1.48         4.34        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        18.74        36.56       144.16       177.04 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP 
       82.85         5.46        46.32        38.99         2.43         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7UC 
       33.90        73.18        78.35        20.42       101.82        17.19 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
        9.34        50.99        45.83        99.91        27.52        20.81 
TCGA-C5-A907 TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A1O9 
       14.73        63.98        87.75        58.88       118.65         8.75 
TCGA-DS-A1OD TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QE 
      127.36         8.28        39.55        31.36        33.30        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A556 
       36.89        26.40        24.56        26.01        24.82        14.89 
TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R8 
       27.29        13.48        26.27         0.39         0.59         1.45 
TCGA-EK-A2RJ TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3HZ 
        1.74        15.22        19.79        15.55        23.84        36.26 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       28.31        35.44        17.75        25.41        16.57        21.67 
TCGA-HM-A6W2 TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JX-A3PZ 
        9.44        78.71        36.36        27.42        21.44        21.11 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MU-A51Y 
       11.28         0.89        12.49        22.52        17.82        28.08 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A73O TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       35.05        17.23        14.07        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QM 
       11.67        93.99        23.97        65.49        32.15        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A958 TCGA-VS-A959 
       40.87        16.64         4.73        33.37        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UT TCGA-VS-A9UU 
       43.40        28.50        29.95        46.92        15.85        14.53 
TCGA-VS-A9V0 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZX-AA5X 
       18.84        15.42        29.26        67.59         3.91 

subtype1 subtype2 subtype3 
    0.13     0.07     0.39 
subtype1 subtype2 subtype3 
  147.39   210.67   177.04 
subtype1 subtype2 subtype3 
   20.63    20.91    24.82 
[1] "0.1 - 147.4 (20.6)" "0.1 - 210.7 (20.9)" "0.4 - 177.0 (24.8)"
D2V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 39 18  4  1
  subtype2 47 24 12  5
  subtype3 55 30  5  4
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       39       47       55
  T2       18       24       30
  T3        4       12        5
  T4        1        5        4
[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"
D2V4, binary
          cls
clus        0  1
  subtype1 36 13
  subtype2 41 26
  subtype3 58 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   13
  subtype2   41   26
  subtype3   58   21
   clus
vv  subtype1 subtype2 subtype3
  0       36       41       58
  1       13       26       21
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 24  4
  subtype2 37  2
  subtype3 55  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    4
  subtype2   37    2
  subtype3   55    4
   clus
vv  subtype1 subtype2 subtype3
  0       24       37       55
  1        4        2        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 16 31
  subtype2 22 53
  subtype3 17 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   31
  subtype2   22   53
  subtype3   17   45
     clus
vv    subtype1 subtype2 subtype3
  NO        16       22       17
  YES       31       53       45
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               28
  subtype2             0                              122
  subtype3             3                              104
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             6
  subtype2                                             0
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  subtype2                                   0
  subtype3                                   2
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         1
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           14
  subtype2                                            0
  subtype3                                            3
D2V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        0        3
  CERVICAL SQUAMOUS CELL CARCINOMA                    28      122      104
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        6        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        0        2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        14        0        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"
D2V8, continuous
D2V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                         4
  subtype2                                4     4                        11
  subtype3                                3     9                        15
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    52
  subtype2                                         2    85
  subtype3                                         0    74
D2V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        4        3
  ASIAN                                            7        4        9
  BLACK OR AFRICAN AMERICAN                        4       11       15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        2        0
  WHITE                                           52       85       74
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
          cls
clus        0  1
  subtype1  7 37
  subtype2  9 68
  subtype3  8 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   37
  subtype2    9   68
  subtype3    8   66
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        9        8
  NOT HISPANIC OR LATINO       37       68       66
[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, continuous
D2V13, binary
          cls
clus        0  1
  subtype1 46 21
  subtype2 76 33
  subtype3 79 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   21
  subtype2   76   33
  subtype3   79   26
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       46       76       79
  WITH TUMOR       21       33       26
[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       G1 G2 G3 G4 GX
  subtype1  7 27 31  0  6
  subtype2  6 62 40  0 10
  subtype3  5 47 49  1  8
D2V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        7        6        5
  G2       27       62       47
  G3       31       40       49
  G4        0        0        1
  GX        6       10        8
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, continuous
D2V16, continuous
D2V17, continuous
D2V18, continuous
D2V19, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2  8  1
  subtype3 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2    8    1
  subtype3   14    2
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           7        8       14
  TREATMENT NOT COMPLETED        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"
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                      10
  subtype2                                   3                      13
  subtype3                                   3                      17
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       7
  subtype3                       0                       3
D2V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        3        3
  OTHER LOCATION, SPECIFY                   10       13       17
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        7        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             2
  subtype3                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                             10
  subtype2                                             10
  subtype3                                              5
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                20
  subtype2                                                                                37
  subtype3                                                                                27
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           30
  subtype2                                                                                           39
  subtype3                                                                                           56
D2V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       39
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       56
[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"
D2V28, binary
          cls
clus        0  1
  subtype1 20 22
  subtype2 20 32
  subtype3 32 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   22
  subtype2   20   32
  subtype3   32   26
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        20       20       32
  PRESENT       22       32       26
[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"
D2V29, continuous
D2V30, continuous
D2V31, binary
          cls
clus        0  1
  subtype1  1 17
  subtype2 31 55
  subtype3 23 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   17
  subtype2   31   55
  subtype3   23   48
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            1       31       23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17       55       48
[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"
D2V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          17         19
  subtype2            3          20         37
  subtype3            5          17         34
D2V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        7        3        5
  FORMER USER        17       20       17
  NEVER USED         19       37       34
[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"
D2V34, continuous
D2V35, binary
          cls
clus        0  1
  subtype1 33  4
  subtype2 32  4
  subtype3 34 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    4
  subtype2   32    4
  subtype3   34   11
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        33       32       34
  PRESENT        4        4       11
[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       CARBOPLATIN CISPLATIN OTHER
  subtype1           2        20     1
  subtype2           3        40     0
  subtype3           2        44     1
D2V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        2        3        2
  CISPLATIN         20       40       44
  OTHER              1        0        1
[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"
D2V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        7        8 
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype3"
D2V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        28        12
  subtype2       4        0         1         1       12        23        13
  subtype3       0        1         0         0       21        27        14
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         3          1          0         9         0
  subtype2        3         2          0          4        17         1
  subtype3        1         4          4          3        18         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          8         0         4
  subtype2          2         22         6         5
  subtype3          1         12         3         3
D2V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA          0        0        1
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          5       12       21
  STAGE IB1        28       23       27
  STAGE IB2        12       13       14
  STAGE II          1        3        1
  STAGE IIA         3        2        4
  STAGE IIA1        1        0        4
  STAGE IIA2        0        4        3
  STAGE IIB         9       17       18
  STAGE III         0        1        0
  STAGE IIIA        0        2        1
  STAGE IIIB        8       22       12
  STAGE IVA         0        6        3
  STAGE IVB         4        5        3
[1] 17  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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 43 14
  subtype2 35  6
  subtype3 55 11
subtype1 subtype2 subtype3 
      57       41       66 
subtype1 subtype2 subtype3 
      14        6       11 
$subtype1
TCGA-DS-A1OC TCGA-EX-A449 TCGA-EX-A69M TCGA-2W-A8YY TCGA-4J-AA1J TCGA-C5-A0TN 
       12.36        14.70         8.32        17.52        17.82        11.44 
TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT 
      144.16        31.40        46.32        38.99        40.93        73.18 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DS-A0VK 
       18.02        17.85        20.42         9.34         1.12        36.76 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A411 
       17.52         8.28        39.55        31.36        25.02        24.56 
TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A97N TCGA-EK-A2H1 
       26.01         7.46        26.79        27.29         0.36        26.27 
TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A3GN 
        1.45         0.07         1.87         1.74        47.77         0.89 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A40J TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ 
       19.79        15.55        14.01        17.75        16.57        21.67 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JX-A5QV TCGA-LP-A4AW TCGA-MU-A5YI 
      129.37        96.95        78.71        20.91         0.89        34.62 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-VS-A8QF 
       17.23        15.95        14.07        19.59        14.60        59.18 
TCGA-VS-A94X TCGA-VS-A9UB TCGA-ZJ-A8QR 
       16.64        29.95        19.13 

$subtype2
TCGA-C5-A8XJ TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1MJ TCGA-C5-A2LY TCGA-C5-A7CK 
      146.86       173.29        30.21         0.46        78.35       134.33 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VL TCGA-DS-A1OA TCGA-DS-A1OD TCGA-EA-A1QT 
       82.06        63.98        55.63        28.90       127.36        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HU TCGA-EA-A44S TCGA-EA-A5ZE 
       37.35        30.90        31.53        33.30        12.13        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2RK 
       27.22        24.00        13.48        60.72         0.43         0.43 
TCGA-EX-A1H5 TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LL 
       20.35        35.44        25.41        14.93       147.39        36.36 
TCGA-JW-A5VL TCGA-LP-A4AX TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-Q1-A6DW 
       15.58        12.49        19.56         8.52        11.38        17.56 
TCGA-Q1-A73Q TCGA-VS-A8EK TCGA-VS-A9UD TCGA-VS-A9V0 TCGA-ZJ-AAXA 
        9.34        27.25        24.30        18.84         1.41 

$subtype3
TCGA-FU-A3TX TCGA-C5-A1M5 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
        1.48        67.46        35.01        57.73        53.16        35.61 
TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 
        3.58        33.90        73.45        83.05       100.14        33.24 
TCGA-C5-A7CG TCGA-C5-A8XI TCGA-C5-A907 TCGA-DG-A2KL TCGA-DS-A0VM TCGA-DS-A0VN 
      210.67         8.35        14.73        44.94       117.99       118.65 
TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD TCGA-EA-A3Y4 
        8.75        28.31        22.98        16.83        13.05        36.89 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EK-A2IP 
       26.40        31.73        24.82        14.89        25.91         6.64 
TCGA-EK-A2IR TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
      113.16         0.39         0.59         0.89         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK TCGA-FU-A23K TCGA-FU-A23L 
        4.24         1.64         0.07         0.49        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3TQ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LI TCGA-IR-A3LK 
       19.04        26.14       137.16        66.81        81.96        29.85 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       21.11       209.59         0.30         0.82        13.35        22.52 
TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A73P 
       17.82         9.17        28.08        19.96        20.84        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PF TCGA-VS-A9U5 TCGA-VS-A9UQ TCGA-WL-A834 
       18.64        22.62        93.99        50.47        41.52        26.01 

subtype1 subtype2 subtype3 
    0.07     0.43     0.07 
subtype1 subtype2 subtype3 
  144.16   173.29   210.67 
subtype1 subtype2 subtype3 
   18.02    27.25    24.33 
[1] "0.1 - 144.2 (18.0)" "0.4 - 173.3 (27.2)" "0.1 - 210.7 (24.3)"
D3V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 34 10  1  1
  subtype2 26  7  3  1
  subtype3 39 15  3  1
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       34       26       39
  T2       10        7       15
  T3        1        3        3
  T4        1        1        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus        0  1
  subtype1 33 11
  subtype2 22  8
  subtype3 38 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   11
  subtype2   22    8
  subtype3   38   19
   clus
vv  subtype1 subtype2 subtype3
  0       33       22       38
  1       11        8       19
[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"
D3V5, binary
          cls
clus        0  1
  subtype1 28  2
  subtype2 25  0
  subtype3 31  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    2
  subtype2   25    0
  subtype3   31    2
   clus
vv  subtype1 subtype2 subtype3
  0       28       25       31
  1        2        0        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"
D3V6, binary
          cls
clus        0  1
  subtype1  7 22
  subtype2  7 17
  subtype3 12 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   22
  subtype2    7   17
  subtype3   12   21
     clus
vv    subtype1 subtype2 subtype3
  NO         7        7       12
  YES       22       17       21
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               51
  subtype2             0                               41
  subtype3             1                               52
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             0
  subtype3                                             2
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   3
  subtype2                                   3
  subtype3                                  10
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         2
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            2
  subtype2                                            1
  subtype3                                            1
D3V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        0        1
  CERVICAL SQUAMOUS CELL CARCINOMA                    51       41       52
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        0        2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  3        3       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         2        1        1
[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"
D3V8, continuous
D3V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         7
  subtype2                                1     7                         1
  subtype3                                1     4                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    42
  subtype2                                         0    32
  subtype3                                         0    51
D3V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        1
  ASIAN                                            4        7        4
  BLACK OR AFRICAN AMERICAN                        7        1        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                           42       32       51
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus        0  1
  subtype1  3 43
  subtype2  5 27
  subtype3  5 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   43
  subtype2    5   27
  subtype3    5   43
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        5        5
  NOT HISPANIC OR LATINO       43       27       43
[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"
D3V12, continuous
D3V13, binary
          cls
clus        0  1
  subtype1 40 14
  subtype2 32  7
  subtype3 47 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   14
  subtype2   32    7
  subtype3   47   15
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       40       32       47
  WITH TUMOR       14        7       15
[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       G1 G2 G3 G4 GX
  subtype1  3 26 25  1  4
  subtype2  2 23 14  0  3
  subtype3  5 26 35  0  1
D3V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        3        2        5
  G2       26       23       26
  G3       25       14       35
  G4        1        0        0
  GX        4        3        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
D3V16, continuous
D3V17, continuous
D3V18, continuous
D3V19, binary
          cls
clus       0 1
  subtype1 9 1
  subtype2 5 1
  subtype3 7 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2    5    1
  subtype3    7    0
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           9        5        7
  TREATMENT NOT COMPLETED        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"
D3V20, continuous
D3V21, continuous
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       5
  subtype2                                   1                       7
  subtype3                                   5                      13
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       2
  subtype2                       0                       1
  subtype3                       0                       4
D3V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        5
  OTHER LOCATION, SPECIFY                    5        7       13
  POSITIVE BLADDER MARGIN                    1        0        0
  POSITIVE VAGINAL MARGIN                    2        1        4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             2
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              2
  subtype2                                              6
  subtype3                                              5
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                13
  subtype2                                                                                12
  subtype3                                                                                21
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           35
  subtype2                                                                                           17
  subtype3                                                                                           27
D3V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       35
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       17
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
[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"
D3V28, binary
          cls
clus        0  1
  subtype1 22 15
  subtype2 15 13
  subtype3 15 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   15
  subtype2   15   13
  subtype3   15   32
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        22       15       15
  PRESENT       15       13       32
[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"
D3V29, continuous
D3V30, continuous
D3V31, binary
          cls
clus        0  1
  subtype1 15 29
  subtype2  6 25
  subtype3 18 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   29
  subtype2    6   25
  subtype3   18   22
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           15        6       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       29       25       22
[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"
D3V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            2          10         16
  subtype2            0           8         16
  subtype3            3          14         19
D3V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        2        0        3
  FORMER USER        10        8       14
  NEVER USED         16       16       19
[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"
D3V34, continuous
D3V35, binary
          cls
clus        0  1
  subtype1 27  3
  subtype2 26  1
  subtype3 31  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    3
  subtype2   26    1
  subtype3   31    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        27       26       31
  PRESENT        3        1        8
[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       CARBOPLATIN CISPLATIN OTHER
  subtype1           0        18     1
  subtype2           1        15     0
  subtype3           2        15     0
D3V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        2
  CISPLATIN         18       15       15
  OTHER              1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V37, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        2        5 
[1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[8] "subtype3" "subtype1"
D3V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        8        15        13
  subtype2       2        0         0         1        8        12         4
  subtype3       1        0         0         0       11        21        11
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         2          1          1         8         0
  subtype2        3         1          0          0         4         0
  subtype3        1         2          3          3         4         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          6         1         1
  subtype2          1          7         2         0
  subtype3          0          6         1         1
D3V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        2        1
  STAGE IA          1        0        0
  STAGE IA1         1        0        0
  STAGE IA2         0        1        0
  STAGE IB          8        8       11
  STAGE IB1        15       12       21
  STAGE IB2        13        4       11
  STAGE II          0        3        1
  STAGE IIA         2        1        2
  STAGE IIA1        1        0        3
  STAGE IIA2        1        0        3
  STAGE IIB         8        4        4
  STAGE III         0        0        1
  STAGE IIIA        0        1        0
  STAGE IIIB        6        7        6
  STAGE IVA         1        2        1
  STAGE IVB         1        0        1
[1] 17  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 = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 25  6
  subtype2 41  7
  subtype3 40  8
  subtype4 14  7
  subtype5 13  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      31       48       48       21       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        7        8        7        3 
$subtype1
TCGA-EX-A449 TCGA-2W-A8YY TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1M7 TCGA-C5-A1MH 
       14.70        17.52        11.44       144.16        46.32        38.99 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7X3 TCGA-EA-A1QS TCGA-EA-A3QE 
       18.02        17.85        20.42         9.34        39.55        25.02 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EK-A2RE 
       26.79        27.29         0.36        26.27         1.45         1.87 
TCGA-EX-A69L TCGA-FU-A40J TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LF 
       19.79        14.01        17.75        16.57        21.67        96.95 
TCGA-LP-A4AW TCGA-MU-A5YI TCGA-Q1-A5R3 TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 
        0.89        34.62        15.95        14.07        19.59        14.60 
TCGA-ZJ-A8QR 
       19.13 

$subtype2
TCGA-EX-A69M TCGA-FU-A3TX TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
        8.32         1.48        17.82        35.01        57.73        53.16 
TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-DG-A2KH 
        3.58        73.18        83.05        33.24       210.67         1.12 
TCGA-DG-A2KL TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD 
       44.94       118.65        28.31        22.98        16.83        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A556 TCGA-EK-A2IR TCGA-EK-A2PK TCGA-EK-A2PM 
       36.89        26.40        14.89       113.16         0.39         0.59 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EX-A8YF 
        4.24         0.07        47.77         1.64         0.07        15.55 
TCGA-FU-A2QG TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK 
       19.04       137.16        66.81       129.37        81.96        29.85 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MU-A51Y TCGA-MU-A8JM 
       20.91         0.30        22.52        17.82        28.08        19.96 
TCGA-MY-A5BF TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-VS-A9UQ TCGA-WL-A834 
       20.84        15.88        18.64        22.62        41.52        26.01 

$subtype3
TCGA-C5-A8XJ TCGA-DS-A1OC TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1MI 
      146.86        12.36       173.29        67.46        30.21        35.61 
TCGA-C5-A1MQ TCGA-C5-A2LZ TCGA-C5-A7CK TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM 
       33.90       100.14       134.33        14.73        82.06        63.98 
TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
      117.99         8.75       127.36        40.87        37.35        31.53 
TCGA-EA-A3HU TCGA-EA-A44S TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       33.30        12.13        25.91        27.25        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2RK TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23K 
       60.72         0.43         0.43         0.49        20.35        12.23 
TCGA-FU-A3TQ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U3 
       26.14        14.93        36.36        15.58       209.59         0.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-Q1-A6DW TCGA-UC-A7PF 
       19.56         9.17         8.52        11.38        17.56        93.99 
TCGA-VS-A8EK TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9V0 
       27.25        59.18        16.64        50.47        24.30        18.84 

$subtype4
TCGA-C5-A1M6 TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A8XI TCGA-DS-A0VK 
       31.40        40.93        73.45        78.35         8.35        36.76 
TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A50E 
       55.63         8.28        31.36        24.56        26.01         7.46 
TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A3GN TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AX 
        6.64         1.74         0.89        78.71        21.11        12.49 
TCGA-MY-A913 TCGA-Q1-A73Q TCGA-VS-A9UB 
       17.23         9.34        29.95 

$subtype5
TCGA-C5-A1MJ TCGA-DS-A1OA TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A4BA 
        0.46        28.90        17.52        30.90        31.73        24.82 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-FU-A23L TCGA-FU-A57G 
       27.22         0.89         0.13        40.96        23.84        35.44 
TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-LP-A7HU TCGA-ZJ-AAXA 
       25.41       147.39        13.35         1.41 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.36     0.07     0.43     0.89     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
  144.16   210.67   209.59    78.71   147.39 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.020   22.570   26.695   24.560   25.115 
[1] "0.4 - 144.2 (18.0)" "0.1 - 210.7 (22.6)" "0.4 - 209.6 (26.7)"
[4] "0.9 - 78.7 (24.6)"  "0.1 - 147.4 (25.1)"
D4V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 19  4  0  0
  subtype2 31  9  2  0
  subtype3 24 11  4  2
  subtype4 13  3  1  1
  subtype5 12  5  0  0
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       19       31       24       13       12
  T2        4        9       11        3        5
  T3        0        2        4        1        0
  T4        0        0        2        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 30 12
  subtype3 19 14
  subtype4 13  6
  subtype5 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   30   12
  subtype3   19   14
  subtype4   13    6
  subtype5   14    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       17       30       19       13       14
  1        4       12       14        6        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 24  1
  subtype3 26  1
  subtype4 12  1
  subtype5 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   24    1
  subtype3   26    1
  subtype4   12    1
  subtype5   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12       24       26       12       10
  1        1        1        1        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"
D4V6, binary
          cls
clus        0  1
  subtype1  7 10
  subtype2  9 16
  subtype3  5 25
  subtype4  3  6
  subtype5  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   10
  subtype2    9   16
  subtype3    5   25
  subtype4    3    6
  subtype5    2    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7        9        5        3        2
  YES       10       16       25        6        3
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               26
  subtype2             2                               35
  subtype3             0                               49
  subtype4             0                               23
  subtype5             0                               11
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   2
  subtype2                                   8
  subtype3                                   1
  subtype4                                   0
  subtype5                                   5
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         2
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            1
  subtype2                                            1
  subtype3                                            1
  subtype4                                            0
  subtype5                                            1
D4V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    26       35       49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  2        8        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        2        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        1        1
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    23       11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        1
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       15       14        6        2 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype4" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
[37] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype3"
D4V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         3
  subtype2                                2     1                         2
  subtype3                                1     4                         3
  subtype4                                0     2                         4
  subtype5                                0     4                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    23
  subtype2                                         0    37
  subtype3                                         0    37
  subtype4                                         0    15
  subtype5                                         0    13
D4V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        1        0
  ASIAN                                            4        1        4        2
  BLACK OR AFRICAN AMERICAN                        3        2        3        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           23       37       37       15
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 0
  ASIAN                                            4
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           13
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
          cls
clus        0  1
  subtype1  1 28
  subtype2  3 29
  subtype3  6 29
  subtype4  1 14
  subtype5  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   28
  subtype2    3   29
  subtype3    6   29
  subtype4    1   14
  subtype5    2   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        3        6        1        2
  NOT HISPANIC OR LATINO       28       29       29       14       13
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
D4V13, binary
          cls
clus        0  1
  subtype1 24  6
  subtype2 36  9
  subtype3 36  9
  subtype4 13  7
  subtype5 10  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    6
  subtype2   36    9
  subtype3   36    9
  subtype4   13    7
  subtype5   10    5
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       24       36       36       13       10
  WITH TUMOR        6        9        9        7        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  2 15 12  0  3
  subtype2  5 16 26  0  2
  subtype3  2 26 17  0  2
  subtype4  1  9 10  1  1
  subtype5  0  9  9  0  0
D4V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        2        5        2        1        0
  G2       15       16       26        9        9
  G3       12       26       17       10        9
  G4        0        0        0        1        0
  GX        3        2        2        1        0
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       11       10        1        3 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype5" "subtype2" "subtype3" "subtype5" "subtype2" "subtype3"
[19] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[25] "subtype3" "subtype3" "subtype2" "subtype1" "subtype5" "subtype3"
D4V16, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       15       14        6        2 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype4" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
[37] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype3"
D4V17, continuous
D4V18, continuous
D4V19, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 6 0
  subtype3 7 1
  subtype4 3 0
  subtype5 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    6    0
  subtype3    7    1
  subtype4    3    0
  subtype5    0    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           5        6        7        3
  TREATMENT NOT COMPLETED        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"
D4V20, continuous
D4V21, continuous
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       3
  subtype2                                   4                      10
  subtype3                                   2                       7
  subtype4                                   0                       3
  subtype5                                   0                       2
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       0
  subtype2                       0                       3
  subtype3                       0                       2
  subtype4                       1                       2
  subtype5                       0                       0
D4V26, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       17       11        6        2 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype4"
[31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        4        2        0
  OTHER LOCATION, SPECIFY                    3       10        7        3
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    0        3        2        2
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             2
  subtype4                                             0
  subtype5                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              2
  subtype2                                              3
  subtype3                                              6
  subtype4                                              1
  subtype5                                              1
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 7
  subtype2                                                                                15
  subtype3                                                                                13
  subtype4                                                                                 5
  subtype5                                                                                 6
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           19
  subtype2                                                                                           23
  subtype3                                                                                           18
  subtype4                                                                                           12
  subtype5                                                                                            7
D4V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       19
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       23
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       18
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       12
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        7
[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"
D4V28, binary
          cls
clus        0  1
  subtype1 13  8
  subtype2 13 22
  subtype3 12 17
  subtype4  6  6
  subtype5  8  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    8
  subtype2   13   22
  subtype3   12   17
  subtype4    6    6
  subtype5    8    7
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        13       13       12        6        8
  PRESENT        8       22       17        6        7
[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"
D4V29, continuous
D4V30, continuous
D4V31, binary
          cls
clus        0  1
  subtype1  7 18
  subtype2 16 14
  subtype3 10 25
  subtype4  6 11
  subtype5  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   18
  subtype2   16   14
  subtype3   10   25
  subtype4    6   11
  subtype5    0    8
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            7       16       10        6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       18       14       25       11
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA            0
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        8
[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"
D4V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           4          8
  subtype2            3          12         13
  subtype3            1           6         18
  subtype4            0           6          8
  subtype5            1           4          4
D4V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        0        3        1        0        1
  FORMER USER         4       12        6        6        4
  NEVER USED          8       13       18        8        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V34, continuous
D4V35, binary
          cls
clus        0  1
  subtype1 16  1
  subtype2 24  3
  subtype3 25  3
  subtype4  9  1
  subtype5 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    1
  subtype2   24    3
  subtype3   25    3
  subtype4    9    1
  subtype5   10    4
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        16       24       25        9       10
  PRESENT        1        3        3        1        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         9     1
  subtype2           1        10     0
  subtype3           0        22     0
  subtype4           0         6     0
  subtype5           2         1     0
D4V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        0        1        0        0        2
  CISPLATIN          9       10       22        6        1
  OTHER              1        0        0        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V37, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        5        2        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D4V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        4         7         9
  subtype2       1        0         0         0        8        20         8
  subtype3       1        0         0         1        8        10         4
  subtype4       1        0         0         0        5         5         3
  subtype5       0        0         0         0        2         6         4
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         1          0          0         3         0
  subtype2        0         1          1          2         3         0
  subtype3        2         1          0          0         8         1
  subtype4        0         1          1          1         2         0
  subtype5        2         1          2          1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          3         0         1
  subtype2          0          3         0         1
  subtype3          1         10         3         0
  subtype4          0          3         1         0
  subtype5          0          0         0         0
D4V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        1        1        0
  STAGE IA          1        0        0        0        0
  STAGE IA1         1        0        0        0        0
  STAGE IA2         0        0        1        0        0
  STAGE IB          4        8        8        5        2
  STAGE IB1         7       20       10        5        6
  STAGE IB2         9        8        4        3        4
  STAGE II          0        0        2        0        2
  STAGE IIA         1        1        1        1        1
  STAGE IIA1        0        1        0        1        2
  STAGE IIA2        0        2        0        1        1
  STAGE IIB         3        3        8        2        0
  STAGE III         0        0        1        0        0
  STAGE IIIA        0        0        1        0        0
  STAGE IIIB        3        3       10        3        0
  STAGE IVA         0        0        3        1        0
  STAGE IVB         1        1        0        0        0
[1] 17  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 46 12
  subtype2 74 24
  subtype3 53 15
  subtype4 46 21
subtype1 subtype2 subtype3 subtype4 
      58       98       68       67 
subtype1 subtype2 subtype3 subtype4 
      12       24       15       21 
$subtype1
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-FU-A3TX TCGA-2W-A8YY TCGA-BI-A0VS TCGA-C5-A1MI 
      146.86        12.59         1.48        17.52        57.04        35.61 
TCGA-C5-A1ML TCGA-C5-A2LX TCGA-C5-A7CK TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT 
       20.91        83.05       134.33         8.35        23.51        20.81 
TCGA-C5-A8ZZ TCGA-DS-A0VK TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OD TCGA-DS-A3LQ 
       20.91        36.76         8.75        28.31       127.36        22.98 
TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       39.55        13.05        26.40        31.73        24.82        14.89 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IR TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 
       27.25        27.22       113.16        19.27         0.59         0.13 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB 
        0.07        20.35        23.84        36.26        20.98        16.14 
TCGA-FU-A57G TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3LH TCGA-JW-A5VH TCGA-JW-A5VK 
       35.44        20.78         9.44        78.71         3.29        20.48 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A5BE TCGA-PN-A8MA 
        0.89         0.30        13.35        34.62        35.05         2.96 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A94W TCGA-VS-A9U6 
        9.34        22.62        46.52        19.96        40.87        43.40 
TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UT 
       24.30        14.53        47.47        15.85 

$subtype2
TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
        0.69        17.82        49.48        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A3HL 
       30.21        38.99         2.43         3.58       100.14        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A901 
      210.67       101.82        15.48       147.35       155.77        17.03 
TCGA-C5-A905 TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
      160.41        44.94        63.98        87.75        58.88        55.63 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       28.90        16.83        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 
       31.36        33.30        25.02        12.13         7.46        25.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2RA 
       27.29        24.00        13.48         0.36         1.51        40.96 
TCGA-EK-A2RB TCGA-EK-A2RK TCGA-EK-A2RN TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ 
        0.30         0.43         2.33        19.04        31.36        26.14 
TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VJ 
       28.31        10.55        21.67        14.93        36.36        21.44 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U3 TCGA-MA-AA3W 
        8.28        18.15       209.59        20.91         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF 
       20.28        19.56         8.52        28.08        19.96        20.84 
TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EH 
       16.41        17.56        93.99        12.16        45.57        32.42 
TCGA-VS-A8EK TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Z 
       27.25        32.15        11.51        59.18        31.27        33.37 
TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV 
       56.35        48.39        45.11        27.25        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       18.25        18.25        17.75        26.01        29.26         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

$subtype3
TCGA-EX-A449 TCGA-EX-A69M TCGA-VS-A9V4 TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 
       14.70         8.32         4.34        23.67        31.40        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       57.73        53.16         0.46        44.22        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-DG-A2KH 
       18.02        17.85        20.35         2.73        50.99         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A5FO 
       95.11        82.06        16.18        17.52        24.56        26.79 
TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK 
        0.39         0.89         4.24        47.77         1.64         0.49 
TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A770 
        7.92        15.55        12.23        16.11        14.01         1.12 
TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       25.41       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LI TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       81.96        28.37        44.61        54.81        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8QA 
       16.14        15.88        18.64        14.60        69.50        36.13 
TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC 
       39.78        58.45        55.50        51.32        50.47        27.12 
TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 
        1.71        47.87        41.52        26.07        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V5 
        5.16        16.24 

$subtype4
TCGA-DS-A1OC TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A1MQ 
       12.36        11.44        18.74         5.46        40.93        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC 
       73.18        73.45        78.35        52.01       154.32        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK 
      131.11        94.95         9.34        13.61        45.83        99.91 
TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A907 TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WI 
       27.52         4.90        14.73       117.99       118.65         8.28 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       36.89        26.01        60.72        26.27         6.64         0.43 
TCGA-EK-A2R8 TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 
        1.45         1.87         1.74         0.10         0.89        15.22 
TCGA-EX-A69L TCGA-GH-A9DA TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL 
       19.79        17.75        29.85        27.42        24.56        15.58 
TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA43 
       21.11        11.28        12.49        17.82         9.17        11.38 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB 
       17.23         9.04        14.07        19.59        11.67        10.03 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 
       23.97        65.49        53.59        16.64         4.73        40.14 
TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       15.68        50.14        29.95        46.92        15.42        67.59 
TCGA-ZJ-A8QR 
       19.13 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.16     0.39     0.10 
subtype1 subtype2 subtype3 subtype4 
  146.86   210.67   147.39   154.32 
subtype1 subtype2 subtype3 subtype4 
  21.800   26.695   24.985   18.740 
[1] "0.1 - 146.9 (21.8)" "0.2 - 210.7 (26.7)" "0.4 - 147.4 (25.0)"
[4] "0.1 - 154.3 (18.7)"
D5V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 24 17  5  3
  subtype2 47 25  8  4
  subtype3 40 14  2  1
  subtype4 29 15  5  2
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       24       47       40       29
  T2       17       25       14       15
  T3        5        8        2        5
  T4        3        4        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"
D5V4, binary
          cls
clus        0  1
  subtype1 26 13
  subtype2 44 26
  subtype3 35 10
  subtype4 28 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   13
  subtype2   44   26
  subtype3   35   10
  subtype4   28   11
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       26       44       35       28
  1       13       26       10       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 25  4
  subtype2 43  1
  subtype3 23  2
  subtype4 25  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    4
  subtype2   43    1
  subtype3   23    2
  subtype4   25    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       25       43       23       25
  1        4        1        2        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1  9 26
  subtype2 16 39
  subtype3 15 30
  subtype4 15 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   26
  subtype2   16   39
  subtype3   15   30
  subtype4   15   32
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         9       16       15       15
  YES       26       39       30       32
[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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               50
  subtype2             0                              103
  subtype3             2                               28
  subtype4             0                               71
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             2
  subtype2                                             0
  subtype3                                             4
  subtype4                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   3
  subtype2                                   0
  subtype3                                  18
  subtype4                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         1
  subtype2                                         0
  subtype3                                         2
  subtype4                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            2
  subtype2                                            0
  subtype3                                           15
  subtype4                                            0
D5V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    50      103       28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        2        0        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  3        0       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            1        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         2        0       15
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     7                         9
  subtype2                                1     7                        10
  subtype3                                0     2                         1
  subtype4                                4     4                        10
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    38
  subtype2                                         0    69
  subtype3                                         0    55
  subtype4                                         2    47
D5V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 2        1        0        4
  ASIAN                                            7        7        2        4
  BLACK OR AFRICAN AMERICAN                        9       10        1       10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           38       69       55       47
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
          cls
clus        0  1
  subtype1  2 39
  subtype2  8 59
  subtype3  5 32
  subtype4  9 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   39
  subtype2    8   59
  subtype3    5   32
  subtype4    9   39
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        8        5        9
  NOT HISPANIC OR LATINO       39       59       32       39
[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"
D5V12, continuous
D5V13, binary
          cls
clus        0  1
  subtype1 36 21
  subtype2 69 22
  subtype3 48 17
  subtype4 45 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   21
  subtype2   69   22
  subtype3   48   17
  subtype4   45   20
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       36       69       48       45
  WITH TUMOR       21       22       17       20
[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"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  2 22 32  1  2
  subtype2  7 62 26  0  6
  subtype3  7 30 25  0  7
  subtype4  2 21 35  0  9
D5V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        2        7        7        2
  G2       22       62       30       21
  G3       32       26       25       35
  G4        1        0        0        0
  GX        2        6        7        9
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, continuous
D5V16, continuous
D5V17, continuous
D5V18, continuous
D5V19, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2 10  1
  subtype3  4  0
  subtype4  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   10    1
  subtype3    4    0
  subtype4    8    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           7       10        4        8
  TREATMENT NOT COMPLETED        0        1        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V20, continuous
D5V21, continuous
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       5
  subtype2                                   2                      16
  subtype3                                   2                      10
  subtype4                                   3                       9
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       4
  subtype2                       1                       5
  subtype3                       0                       3
  subtype4                       0                       0
D5V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        2        3
  OTHER LOCATION, SPECIFY                    5       16       10        9
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    4        5        3        0
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             2
  subtype3                                             1
  subtype4                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              6
  subtype2                                              8
  subtype3                                              7
  subtype4                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                22
  subtype2                                                                                34
  subtype3                                                                                19
  subtype4                                                                                 7
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           23
  subtype2                                                                                           37
  subtype3                                                                                           30
  subtype4                                                                                           34
D5V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       23
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       34
[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"
D5V28, binary
          cls
clus        0  1
  subtype1 15 19
  subtype2 25 29
  subtype3 18 21
  subtype4 13 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   19
  subtype2   25   29
  subtype3   18   21
  subtype4   13   10
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        15       25       18       13
  PRESENT       19       29       21       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V29, continuous
D5V30, continuous
D5V31, binary
          cls
clus        0  1
  subtype1 15 22
  subtype2 21 53
  subtype3  1 16
  subtype4 18 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   22
  subtype2   21   53
  subtype3    1   16
  subtype4   18   28
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA           15       21        1       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       22       53       16       28
[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"
D5V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0          13         20
  subtype2            3          15         31
  subtype3            8          15         18
  subtype4            4          10         20
D5V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        0        3        8        4
  FORMER USER        13       15       15       10
  NEVER USED         20       31       18       20
[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"
D5V34, continuous
D5V35, binary
          cls
clus        0  1
  subtype1 19  6
  subtype2 32  9
  subtype3 28  4
  subtype4 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    6
  subtype2   32    9
  subtype3   28    4
  subtype4   20    0
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        19       32       28       20
  PRESENT        6        9        4        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           3        16     0
  subtype2           2        34     0
  subtype3           1        20     1
  subtype4           1        32     1
D5V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  CARBOPLATIN        3        2        1        1
  CISPLATIN         16       34       20       32
  OTHER              0        0        1        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V37, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        9        1        4 
 [1] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
 [7] "subtype4" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2"
D5V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        5        13         9
  subtype2       1        0         0         1       15        22         9
  subtype3       1        0         0         0        5        31        10
  subtype4       2        0         0         0       13        11        11
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         1          3          4         7         0
  subtype2        4         2          1          2        12         1
  subtype3        0         2          0          0        10         0
  subtype4        0         4          1          1        14         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          1          8         2         3
  subtype2          0         20         4         5
  subtype3          0          5         1         3
  subtype4          1          9         2         1
D5V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        1        2
  STAGE IA          1        0        0        0
  STAGE IA1         1        0        0        0
  STAGE IA2         0        1        0        0
  STAGE IB          5       15        5       13
  STAGE IB1        13       22       31       11
  STAGE IB2         9        9       10       11
  STAGE II          1        4        0        0
  STAGE IIA         1        2        2        4
  STAGE IIA1        3        1        0        1
  STAGE IIA2        4        2        0        1
  STAGE IIB         7       12       10       14
  STAGE III         0        1        0        0
  STAGE IIIA        1        0        0        1
  STAGE IIIB        8       20        5        9
  STAGE IVA         2        4        1        2
  STAGE IVB         3        5        3        1
[1] 17  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  53  17
  subtype2 143  42
  subtype3  23  13
subtype1 subtype2 subtype3 
      70      185       36 
subtype1 subtype2 subtype3 
      17       42       13 
$subtype1
TCGA-EX-A449 TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
       14.70         4.34        17.52        31.40        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       35.61         0.46        44.22        38.43        33.24        18.02 
TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.35         2.73        20.81         1.12        95.11        82.06 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       16.18        17.52        26.40        31.73        24.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK 
       26.79        27.22         0.89        47.77         1.64         0.49 
TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J 
        7.92        15.55        12.23        16.11        36.26        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       35.44         1.12         9.44       137.16        66.81        96.95 
TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD 
       81.96         3.29        28.37        44.61        13.35        54.81 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S 
        2.96        15.58        16.14        15.88        18.64        22.62 
TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ 
       69.50        19.96        36.13        39.78        58.45         1.71 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       14.53        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 
       67.20        18.84         5.16        16.24 

$subtype2
TCGA-C5-A8XJ TCGA-DS-A1OC TCGA-EK-A2GZ TCGA-EX-A69M TCGA-FU-A3TX TCGA-ZJ-AAX4 
      146.86        12.36        12.59         8.32         1.48         0.69 
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI 
       17.82        49.48        57.04        23.67        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       46.32        30.21        38.99         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A3HL 
        3.58        83.05        78.35       100.14        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
      210.67       154.32       101.82       134.33        15.48       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
      155.77       131.11        94.95        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A905 TCGA-DG-A2KL 
        8.35        23.51        20.91        17.03       160.41        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OD TCGA-DS-A3LQ 
      118.65         8.75        28.90        28.31       127.36        22.98 
TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.83        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S 
       31.36        33.30        13.05        25.02        24.56        12.13 
TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        25.91        27.29        27.25        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PI 
        0.36        60.72         6.64       113.16         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.43         0.59         0.13        40.96         0.30         4.24 
TCGA-EK-A2RE TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 
        1.87         0.43         2.33         0.07         0.10        20.35 
TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.79        23.84        19.04        31.36        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       16.14        28.31        10.55        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
       14.93       147.39       129.37        29.85        36.36        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       21.44        20.48        15.58         8.28        18.15       209.59 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       20.91        11.28         0.89         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       20.28        17.82        19.56         9.17         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R2 
       28.08        34.62        19.96        35.05        20.84        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-R2-A69V 
       15.95         9.04        17.56        14.07         9.34        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       14.60        93.99        12.16        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        27.25        65.49        32.15        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 
       31.27        40.87        33.37        40.14        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       55.50        50.14        51.32        50.47        43.40        48.39 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU 
       27.12        24.30        46.92        45.11        27.25        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ 
        3.42        18.25        18.25        17.75        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

$subtype3
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MQ TCGA-C5-A2LT 
       11.44        18.74         5.46        53.16        33.90        73.18 
TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A8XK TCGA-C5-A8YR 
       73.45        52.01        17.19         9.34        99.91        27.52 
TCGA-C5-A902 TCGA-C5-A907 TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H1 
        4.90        14.73         8.28        36.89        26.01        26.27 
TCGA-EK-A2PK TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-GH-A9DA 
        0.39         1.45         1.74         0.89        15.22        17.75 
TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-UC-A7PD 
       78.71        27.42        21.11        12.49        17.23        11.67 
TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-AA62 
       10.03        53.59        16.64         4.73        29.95        15.42 

subtype1 subtype2 subtype3 
    0.46     0.07     0.39 
subtype1 subtype2 subtype3 
  137.16   210.67    99.91 
subtype1 subtype2 subtype3 
   20.58    24.56    17.21 
[1] "0.5 - 137.2 (20.6)" "0.1 - 210.7 (24.6)" "0.4 - 99.9 (17.2)" 
D6V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 39 20  3  2
  subtype2 86 42 16  8
  subtype3 15  9  1  0
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       39       86       15
  T2       20       42        9
  T3        3       16        1
  T4        2        8        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 38 13
  subtype2 78 42
  subtype3 17  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   13
  subtype2   78   42
  subtype3   17    5
   clus
vv  subtype1 subtype2 subtype3
  0       38       78       17
  1       13       42        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 27  5
  subtype2 77  3
  subtype3 12  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    5
  subtype2   77    3
  subtype3   12    2
   clus
vv  subtype1 subtype2 subtype3
  0       27       77       12
  1        5        3        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"
D6V6, binary
          cls
clus        0  1
  subtype1 14 33
  subtype2 35 79
  subtype3  6 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   33
  subtype2   35   79
  subtype3    6   15
     clus
vv    subtype1 subtype2 subtype3
  NO        14       35        6
  YES       33       79       15
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               22
  subtype2             0                              193
  subtype3             0                               37
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  21
  subtype2                                   0
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           16
  subtype2                                            1
  subtype3                                            0
D6V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    22      193       37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 21        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        16        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"
D6V8, continuous
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                         3
  subtype2                                4    13                        20
  subtype3                                2     1                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    53
  subtype2                                         2   130
  subtype3                                         0    26
D6V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        4        2
  ASIAN                                            6       13        1
  BLACK OR AFRICAN AMERICAN                        3       20        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        2        0
  WHITE                                           53      130       26
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
          cls
clus         0   1
  subtype1   6  38
  subtype2  16 109
  subtype3   2  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   38
  subtype2   16  109
  subtype3    2   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       16        2
  NOT HISPANIC OR LATINO       38      109       22
[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"
D6V12, continuous
D6V13, binary
          cls
clus         0   1
  subtype1  45  22
  subtype2 130  46
  subtype3  23  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   22
  subtype2  130   46
  subtype3   23   12
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       45      130       23
  WITH TUMOR       22       46       12
[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       G1 G2 G3 G4 GX
  subtype1  7 30 29  0  6
  subtype2 10 93 69  0 16
  subtype3  1 12 20  1  2
D6V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        7       10        1
  G2       30       93       12
  G3       29       69       20
  G4        0        0        1
  GX        6       16        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, continuous
D6V16, continuous
D6V17, continuous
D6V18, continuous
D6V19, binary
          cls
clus        0  1
  subtype1  3  0
  subtype2 20  2
  subtype3  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2   20    2
  subtype3    6    1
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           3       20        6
  TREATMENT NOT COMPLETED        0        2        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"
D6V20, continuous
D6V21, continuous
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       9
  subtype2                                   5                      26
  subtype3                                   2                       5
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       9
  subtype3                       0                       1
D6V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        5        2
  OTHER LOCATION, SPECIFY                    9       26        5
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        9        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             2
  subtype3                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              8
  subtype2                                             15
  subtype3                                              2
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                19
  subtype2                                                                                61
  subtype3                                                                                 2
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           34
  subtype2                                                                                           72
  subtype3                                                                                           18
D6V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       34
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       72
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       18
[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"
D6V28, binary
          cls
clus        0  1
  subtype1 23 21
  subtype2 39 50
  subtype3  9  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   21
  subtype2   39   50
  subtype3    9    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       39        9
  PRESENT       21       50        8
[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"
D6V29, continuous
D6V30, continuous
D6V31, binary
          cls
clus        0  1
  subtype1  0 17
  subtype2 47 89
  subtype3  8 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   17
  subtype2   47   89
  subtype3    8   13
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       47        8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17       89       13
[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"
D6V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          17         21
  subtype2            4          32         59
  subtype3            4           4          9
D6V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        7        4        4
  FORMER USER        17       32        4
  NEVER USED         21       59        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V34, continuous
D6V35, binary
          cls
clus        0  1
  subtype1 31  6
  subtype2 56 13
  subtype3 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    6
  subtype2   56   13
  subtype3   12    0
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        31       56       12
  PRESENT        6       13        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           3        22     1
  subtype2           4        67     0
  subtype3           0        13     1
D6V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        3        4        0
  CISPLATIN         22       67       13
  OTHER              1        0        1
[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"
D6V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1       13        3 
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2"
D6V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        6        28        10
  subtype2       4        1         1         1       24        44        20
  subtype3       0        0         0         0        8         5         9
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         3          1          2         8         0
  subtype2        4         3          2          4        30         1
  subtype3        0         3          2          1         5         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          6         1         5
  subtype2          2         33         8         7
  subtype3          0          3         0         0
D6V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA          0        1        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          6       24        8
  STAGE IB1        28       44        5
  STAGE IB2        10       20        9
  STAGE II          1        4        0
  STAGE IIA         3        3        3
  STAGE IIA1        1        2        2
  STAGE IIA2        2        4        1
  STAGE IIB         8       30        5
  STAGE III         0        1        0
  STAGE IIIA        0        2        0
  STAGE IIIB        6       33        3
  STAGE IVA         1        8        0
  STAGE IVB         5        7        0
[1] 17  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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 81 25
  subtype2 58 17
  subtype3 83 30
subtype1 subtype2 subtype3 
     106       75      113 
subtype1 subtype2 subtype3 
      25       17       30 
$subtype1
TCGA-C5-A8XJ TCGA-EX-A449 TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1BM TCGA-C5-A1M6 
      146.86        14.70         4.34        17.52        82.85        31.40 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1ML 
       30.21        35.01        57.73        53.16        35.61        20.91 
TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CM 
       44.22        38.43        33.24        18.02       210.67        20.35 
TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 TCGA-DG-A2KH TCGA-DG-A2KJ 
        2.73        27.52         4.90       160.41         1.12        95.11 
TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A410 TCGA-EA-A439 
       82.06        16.18         8.28        13.05        26.40        31.73 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A6QX 
       24.82        14.89        26.79        25.91        27.22        24.00 
TCGA-EK-A2IR TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A69L 
      113.16         0.89        47.77         1.64         0.49        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G 
       15.55        12.23        36.26        16.14        14.01        35.44 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LI TCGA-JW-A5VH 
        1.12         9.44       137.16        66.81        81.96         3.29 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A5U2 
       20.48        28.37        18.15        44.61        20.91         0.30 
TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.35        20.28        19.56        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
        2.96        15.58        16.14        17.56        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       18.64        22.62        69.50        10.03        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A952 TCGA-VS-A953 
       19.96        32.15        36.13        11.51        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       56.35        55.50        51.32        43.40        48.39        28.50 
TCGA-VS-A9UD TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       24.30         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-ZJ-AAXU 
        5.16        17.75        16.24         0.16 

$subtype2
TCGA-FU-A3TX TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1M5 
        1.48        17.82        49.48        23.67        68.84        67.46 
TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
        0.46         3.58        17.85        20.42       101.82       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ 
      147.35       155.77        50.99         8.35        20.81        20.91 
TCGA-C5-A901 TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       17.03        44.94        63.98        58.88        36.76        55.63 
TCGA-DS-A1OA TCGA-DS-A1OD TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HR 
       28.90       127.36        16.83        17.52        39.55        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD 
       31.53        31.36        24.56        12.13         7.46        27.29 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2R8 TCGA-EK-A2R9 
       27.25        13.48         0.36        19.27         1.45         0.13 
TCGA-EK-A2RC TCGA-EK-A2RK TCGA-EK-A2RO TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3NI 
        4.24         0.43         0.07         7.92        16.11        20.98 
TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       28.31        25.41        16.57        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-LP-A4AU TCGA-LP-A4AW 
      147.39       129.37        96.95        78.71        11.28         0.89 
TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-UC-A7PF 
       22.52        11.38        28.08        34.62        16.41        93.99 
TCGA-UC-A7PG TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9V2 
       12.16        31.27        40.87        41.52        15.85        18.25 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       29.26         1.41         3.91 

$subtype3
TCGA-DS-A1OC TCGA-EK-A2GZ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-BI-A0VS TCGA-C5-A0TN 
       12.36        12.59         8.32         0.69        57.04        11.44 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04       173.29         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MQ 
       19.86        46.32        38.99         2.43        40.93        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD 
       73.18        73.45        83.05        78.35       100.14        52.01 
TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      154.32        15.48        17.19       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A907 TCGA-DR-A0ZL 
       13.61        45.83        99.91        23.51        14.73        87.75 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-EA-A1QT 
      117.99       118.65         8.75        28.31        22.98        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 
       37.35        33.30        25.02        36.89        26.01        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51         0.39         0.43         0.59 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN 
       40.96         0.30         0.07         1.87         1.74         2.33 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG 
        0.10         0.89        20.35        15.22        23.84        19.04 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-GH-A9DA TCGA-IR-A3LK TCGA-IR-A3LL 
       31.36        26.14        10.55        17.75        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ 
       27.42        24.56        21.44        15.58         8.28        21.11 
TCGA-JX-A3Q0 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 
      209.59        12.49         0.82        17.82         9.17         8.52 
TCGA-MU-A8JM TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V 
       19.96        17.23        15.95         9.04        14.07        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL 
       14.60        11.67        32.42        23.97        27.25        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       53.59        59.18        39.78        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       40.14        50.14        50.47        29.95        27.12        46.92 
TCGA-VS-A9UI TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       45.11        15.42        26.01        67.59        19.13 

subtype1 subtype2 subtype3 
    0.16     0.07     0.07 
subtype1 subtype2 subtype3 
  210.67   155.77   209.59 
subtype1 subtype2 subtype3 
  21.765   21.670   23.970 
[1] "0.2 - 210.7 (21.8)" "0.1 - 155.8 (21.7)" "0.1 - 209.6 (24.0)"
D7V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 53 28 10  6
  subtype2 46 14  3  1
  subtype3 42 30  8  3
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       53       46       42
  T2       28       14       30
  T3       10        3        8
  T4        6        1        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus        0  1
  subtype1 48 18
  subtype2 40 22
  subtype3 47 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   18
  subtype2   40   22
  subtype3   47   20
   clus
vv  subtype1 subtype2 subtype3
  0       48       40       47
  1       18       22       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 39  7
  subtype2 36  1
  subtype3 41  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    7
  subtype2   36    1
  subtype3   41    2
   clus
vv  subtype1 subtype2 subtype3
  0       39       36       41
  1        7        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"
D7V6, binary
          cls
clus        0  1
  subtype1 23 54
  subtype2 13 28
  subtype3 19 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   54
  subtype2   13   28
  subtype3   19   47
     clus
vv    subtype1 subtype2 subtype3
  NO        23       13       19
  YES       54       28       47
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               66
  subtype2             1                               68
  subtype3             0                              120
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  17
  subtype2                                   4
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           12
  subtype2                                            4
  subtype3                                            1
D7V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    66       68      120
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 17        4        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        12        4        1
[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"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        10
  subtype2                                1     8                         6
  subtype3                                6     4                        14
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    73
  subtype2                                         0    54
  subtype3                                         2    84
D7V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        6
  ASIAN                                            8        8        4
  BLACK OR AFRICAN AMERICAN                       10        6       14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           73       54       84
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
          cls
clus        0  1
  subtype1  7 57
  subtype2  5 46
  subtype3 12 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   57
  subtype2    5   46
  subtype3   12   68
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        5       12
  NOT HISPANIC OR LATINO       57       46       68
[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"
D7V12, continuous
D7V13, binary
          cls
clus        0  1
  subtype1 69 31
  subtype2 54 17
  subtype3 78 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   31
  subtype2   54   17
  subtype3   78   32
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       69       54       78
  WITH TUMOR       31       17       32
[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       G1 G2 G3 G4 GX
  subtype1  8 42 43  0 14
  subtype2  8 41 27  1  1
  subtype3  2 53 50  0  9
D7V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        8        8        2
  G2       42       41       53
  G3       43       27       50
  G4        0        1        0
  GX       14        1        9
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, continuous
D7V16, continuous
D7V17, continuous
D7V18, continuous
D7V19, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2  6  0
  subtype3 16  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2    6    0
  subtype3   16    3
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           7        6       16
  TREATMENT NOT COMPLETED        0        0        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"
D7V20, continuous
D7V21, continuous
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                      10
  subtype2                                   1                      16
  subtype3                                   6                      14
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       7
  subtype3                       0                       3
D7V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        6
  OTHER LOCATION, SPECIFY                   10       16       14
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        7        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             1
  subtype2                                             1
  subtype3                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                             12
  subtype2                                              6
  subtype3                                              7
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                26
  subtype2                                                                                26
  subtype3                                                                                32
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           48
  subtype2                                                                                           30
  subtype3                                                                                           47
D7V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       48
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       47
[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"
D7V28, binary
          cls
clus        0  1
  subtype1 25 29
  subtype2 22 29
  subtype3 25 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   29
  subtype2   22   29
  subtype3   25   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        25       22       25
  PRESENT       29       29       22
[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"
D7V29, continuous
D7V30, continuous
D7V31, binary
          cls
clus        0  1
  subtype1  6 34
  subtype2 18 32
  subtype3 31 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   34
  subtype2   18   32
  subtype3   31   54
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            6       18       31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       34       32       54
[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"
D7V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            8          22         36
  subtype2            3          15         19
  subtype3            4          17         35
D7V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        8        3        4
  FORMER USER        22       15       17
  NEVER USED         36       19       35
[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"
D7V34, continuous
D7V35, binary
          cls
clus        0  1
  subtype1 35  7
  subtype2 32  8
  subtype3 32  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    7
  subtype2   32    8
  subtype3   32    4
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        35       32       32
  PRESENT        7        8        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           3        39     0
  subtype2           1        20     0
  subtype3           3        45     2
D7V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        3        1        3
  CISPLATIN         39       20       45
  OTHER              0        0        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"
D7V37, continuous
D7V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       3        0         0         0       10        30        17
  subtype2       0        1         1         1        8        28        11
  subtype3       2        0         0         0       20        20        11
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         2          1          5        11         0
  subtype2        1         3          2          1         6         0
  subtype3        3         4          2          1        27         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          2         13         4         9
  subtype2          0         10         2         1
  subtype3          1         19         3         2
D7V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        2
  STAGE IA          0        1        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB         10        8       20
  STAGE IB1        30       28       20
  STAGE IB2        17       11       11
  STAGE II          1        1        3
  STAGE IIA         2        3        4
  STAGE IIA1        1        2        2
  STAGE IIA2        5        1        1
  STAGE IIB        11        6       27
  STAGE III         0        0        1
  STAGE IIIA        2        0        1
  STAGE IIIB       13       10       19
  STAGE IVA         4        2        3
  STAGE IVB         9        1        2
[1] 17  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 44 15
  subtype2 76 21
  subtype3 53 17
  subtype4 17  7
  subtype5 32 12
subtype1 subtype2 subtype3 subtype4 subtype5 
      59       97       70       24       44 
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       21       17        7       12 
$subtype1
TCGA-EX-A449 TCGA-VS-A9V4 TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI 
       14.70         4.34        17.52        31.40        57.73        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A7CM 
        0.46        44.22        38.43        33.24        17.85        20.35 
TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF 
        2.73        20.81         1.12        95.11        82.06        16.18 
TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2RL 
       17.52        31.73        24.82        14.89        26.79        47.77 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO 
        1.64         0.49         7.92        15.55        12.23        16.11 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       14.01        35.44         1.12         9.44       137.16        66.81 
TCGA-IR-A3LF TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A6DV 
       96.95        28.37        44.61        13.35        15.58        16.14 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH 
       15.88        18.64        22.62        69.50        36.13        39.78 
TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       58.45         1.71        14.53        47.87        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 
       15.85        67.20        18.84         5.16        16.24 

$subtype2
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-4J-AA1J TCGA-C5-A1BM 
      146.86        12.59         8.32         0.69        17.82        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML TCGA-C5-A2LX TCGA-C5-A2LZ 
       19.86        30.21        53.16        20.91        83.05       100.14 
TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XH 
      154.32        15.48       131.11        94.95        13.61        45.83 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A902 
        8.35        99.91        23.51        20.91        17.03         4.90 
TCGA-C5-A905 TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QE 
      160.41        28.31        22.98        30.90        33.30        25.02 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A6QX TCGA-EK-A2IR 
       24.56        12.13         7.46        25.91        24.00       113.16 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE 
        1.51         0.59         0.89        40.96         0.07         1.87 
TCGA-EK-A2RN TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ 
        2.33         0.89        19.79        19.04        31.36        26.14 
TCGA-FU-A3WB TCGA-FU-A5XV TCGA-HG-A9SC TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VJ 
       16.14        10.55        16.57        81.96        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.48         8.28        18.15        20.91         0.30         0.82 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BD 
       20.28        19.56         8.52        11.38        19.96        54.81 
TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-UC-A7PG 
       20.84        15.95        17.56        14.07         9.34        12.16 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC 
       45.57        32.42        27.25        65.49        32.15        11.51 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       33.37        40.14        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD 
       51.32        50.47        43.40        48.39        28.50        24.30 
TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-WL-A834 
       27.25        14.53         3.42        18.25        17.75        26.01 
TCGA-ZJ-AAXU 
        0.16 

$subtype3
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 
       49.48        23.67        68.84        36.56       177.04        67.46 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LY 
       46.32        38.99         2.43        40.93         3.58        78.35 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE 
       20.42       210.67       101.82       134.33       147.35       155.77 
TCGA-C5-A7XC TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.99        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS 
       55.63       117.99         8.75        28.90        16.83        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5ZD 
       40.87        37.35        31.53        31.36        13.05        27.29 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       27.25        13.48         0.36         1.45         0.13         4.24 
TCGA-EK-A2RK TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.43         0.07        20.35        20.98        28.31        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK 
       21.67        20.78        14.93       147.39       129.37        29.85 
TCGA-IR-A3LL TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE 
       36.36         0.89        22.52        28.08        34.62        35.05 
TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PF TCGA-VS-A8Q9 TCGA-VS-A8QM TCGA-VS-A94W 
       16.41        19.59        93.99        53.59        31.27        40.87 
TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       18.25        29.26         1.41         3.91 

$subtype4
TCGA-DS-A1OC TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A7X3 TCGA-C5-A8YR TCGA-DS-A0VN 
       12.36        57.04       173.29         9.34        27.52       118.65 
TCGA-EA-A410 TCGA-EA-A5ZF TCGA-EK-A2PI TCGA-EK-A2RB TCGA-EK-A2RJ TCGA-FU-A23L 
       26.40        27.22        19.27         0.30         1.74        23.84 
TCGA-FU-A3HZ TCGA-JW-A5VH TCGA-JX-A3Q0 TCGA-MA-AA41 TCGA-PN-A8MA TCGA-Q1-A6DT 
       36.26         3.29       209.59         9.17         2.96         9.04 
TCGA-VS-A8EC TCGA-VS-A94X TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UP TCGA-ZJ-A8QR 
       46.52        16.64        27.12        45.11        47.47        19.13 

$subtype5
TCGA-FU-A3TX TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 
        1.48        11.44        18.74       144.16         5.46        35.01 
TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7UC 
       33.90        73.18        73.45        52.01        18.02        17.19 
TCGA-C5-A907 TCGA-DS-A1OD TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 
       14.73       127.36         8.28        36.89        26.01        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A3GJ TCGA-EX-A3L1 
       26.27         6.64         0.39         0.43         0.10        15.22 
TCGA-GH-A9DA TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU 
       17.75        78.71        27.42        15.58        21.11        11.28 
TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB 
       12.49        17.82        17.23        14.60        11.67        10.03 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-A9UH 
       23.97        19.96        59.18         4.73        29.95        46.92 
TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       15.42        67.59 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.07     0.07     0.30     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  137.16   160.41   210.67   209.59   144.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.840   20.910   31.315   25.120   17.920 
[1] "0.5 - 137.2 (18.8)" "0.1 - 160.4 (20.9)" "0.1 - 210.7 (31.3)"
[4] "0.3 - 209.6 (25.1)" "0.1 - 144.2 (17.9)"
D8V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 35 13  2  1
  subtype2 32 29 12  6
  subtype3 47 11  2  1
  subtype4  8  9  2  1
  subtype5 19 10  3  1
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       35       32       47        8       19
  T2       13       29       11        9       10
  T3        2       12        2        2        3
  T4        1        6        1        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"
D8V4, binary
          cls
clus        0  1
  subtype1 32 10
  subtype2 33 22
  subtype3 38 20
  subtype4 11  2
  subtype5 21  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   10
  subtype2   33   22
  subtype3   38   20
  subtype4   11    2
  subtype5   21    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       32       33       38       11       21
  1       10       22       20        2        6
[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"
D8V5, binary
          cls
clus        0  1
  subtype1 18  2
  subtype2 29  2
  subtype3 38  1
  subtype4 12  2
  subtype5 19  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    2
  subtype2   29    2
  subtype3   38    1
  subtype4   12    2
  subtype5   19    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       18       29       38       12       19
  1        2        2        1        2        3
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 11 28
  subtype2 17 51
  subtype3 14 19
  subtype4  6 11
  subtype5  7 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   28
  subtype2   17   51
  subtype3   14   19
  subtype4    6   11
  subtype5    7   20
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        11       17       14        6        7
  YES       28       51       19       11       20
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               13
  subtype2             1                               99
  subtype3             0                               74
  subtype4             0                               24
  subtype5             0                               44
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             1
  subtype3                                             0
  subtype4                                             1
  subtype5                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   1
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           16
  subtype2                                            0
  subtype3                                            0
  subtype4                                            1
  subtype5                                            0
D8V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    13       99       74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        16        0        0
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    24       44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        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"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         2
  subtype2                                3     5                        13
  subtype3                                1     6                         7
  subtype4                                1     2                         3
  subtype5                                3     2                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    45
  subtype2                                         0    66
  subtype3                                         0    51
  subtype4                                         1    17
  subtype5                                         1    32
D8V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        3        1        1
  ASIAN                                            5        5        6        2
  BLACK OR AFRICAN AMERICAN                        2       13        7        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           45       66       51       17
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 3
  ASIAN                                            2
  BLACK OR AFRICAN AMERICAN                        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           32
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus        0  1
  subtype1  4 31
  subtype2 10 53
  subtype3  3 50
  subtype4  3 16
  subtype5  4 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   31
  subtype2   10   53
  subtype3    3   50
  subtype4    3   16
  subtype5    4   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4       10        3        3        4
  NOT HISPANIC OR LATINO       31       53       50       16       21
[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"
D8V12, continuous
D8V13, binary
          cls
clus        0  1
  subtype1 40 17
  subtype2 67 26
  subtype3 51 16
  subtype4 14  9
  subtype5 29 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   17
  subtype2   67   26
  subtype3   51   16
  subtype4   14    9
  subtype5   29   12
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       40       67       51       14       29
  WITH TUMOR       17       26       16        9       12
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 27 21  0  6
  subtype2  4 46 38  0  8
  subtype3  6 39 28  0  1
  subtype4  0 14  9  0  3
  subtype5  2 10 24  1  6
D8V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        6        4        6        0        2
  G2       27       46       39       14       10
  G3       21       38       28        9       24
  G4        0        0        0        0        1
  GX        6        8        1        3        6
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
D8V16, continuous
D8V17, continuous
D8V18, continuous
D8V19, binary
          cls
clus       0 1
  subtype1 3 0
  subtype2 7 0
  subtype3 9 1
  subtype4 2 0
  subtype5 8 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    7    0
  subtype3    9    1
  subtype4    2    0
  subtype5    8    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  COMPLETED AS PLANNED           3        7        9        2        8
  TREATMENT NOT COMPLETED        0        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"
D8V20, continuous
D8V21, continuous
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       7
  subtype2                                   3                       8
  subtype3                                   3                      16
  subtype4                                   0                       2
  subtype5                                   2                       7
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       4
  subtype3                       0                       5
  subtype4                       0                       0
  subtype5                       0                       1
D8V26, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       16       24        2       10 
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype5" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype5"
[13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype5" "subtype1"
[19] "subtype5" "subtype5" "subtype2" "subtype1" "subtype5" "subtype3"
[25] "subtype3" "subtype3" "subtype5" "subtype2" "subtype1" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype5" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype1" "subtype3" "subtype5" "subtype2" "subtype3"
[55] "subtype3" "subtype2" "subtype5" "subtype1" "subtype1" "subtype2"
[61] "subtype3"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0        3        3        2
  OTHER LOCATION, SPECIFY                    7        8       16        7
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        4        5        1
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             1
  subtype4                                             0
  subtype5                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              5
  subtype2                                              9
  subtype3                                              5
  subtype4                                              4
  subtype5                                              2
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                16
  subtype2                                                                                29
  subtype3                                                                                30
  subtype4                                                                                 5
  subtype5                                                                                 4
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           30
  subtype2                                                                                           37
  subtype3                                                                                           23
  subtype4                                                                                            9
  subtype5                                                                                           26
D8V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       23
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        9
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       26
[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"
D8V28, binary
          cls
clus        0  1
  subtype1 21 16
  subtype2 17 24
  subtype3 19 29
  subtype4  5  3
  subtype5 10  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   16
  subtype2   17   24
  subtype3   19   29
  subtype4    5    3
  subtype5   10    8
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        21       17       19        5       10
  PRESENT       16       24       29        3        8
[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"
D8V29, continuous
D8V30, continuous
D8V31, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2 21 46
  subtype3 20 34
  subtype4  4 12
  subtype5 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2   21   46
  subtype3   20   34
  subtype4    4   12
  subtype5   10   17
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       21       20        4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       11       46       34       12
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA           10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17
[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"
D8V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          14         18
  subtype2            4          17         33
  subtype3            1          14         19
  subtype4            0           5          7
  subtype5            4           4         13
D8V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        6        4        1        0        4
  FORMER USER        14       17       14        5        4
  NEVER USED         18       33       19        7       13
[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"
D8V34, continuous
D8V35, binary
          cls
clus        0  1
  subtype1 27  4
  subtype2 22  5
  subtype3 32  8
  subtype4  5  2
  subtype5 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    4
  subtype2   22    5
  subtype3   32    8
  subtype4    5    2
  subtype5   13    0
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        27       22       32        5       13
  PRESENT        4        5        8        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       CARBOPLATIN CISPLATIN OTHER
  subtype1           2        18     1
  subtype2           2        36     0
  subtype3           2        20     0
  subtype4           1         8     0
  subtype5           0        22     1
D8V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        2        2        2        1        0
  CISPLATIN         18       36       20        8       22
  OTHER              1        0        0        0        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype5 
       1        5        8        3 
 [1] "subtype5" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [7] "subtype5" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype5" "subtype3"
D8V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        26         9
  subtype2       2        0         0         0        7        17        12
  subtype3       0        1         1         1       13        25         8
  subtype4       2        0         0         0        6         1         2
  subtype5       0        0         0         0        7         9         8
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         2          1          0         5         0
  subtype2        3         1          0          3        18         0
  subtype3        1         2          1          1         5         0
  subtype4        0         1          1          2         5         1
  subtype5        0         3          2          1        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          6         1         3
  subtype2          3         19         5         6
  subtype3          0         11         2         1
  subtype4          0          3         0         2
  subtype5          0          3         1         0
D8V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        2        0        2        0
  STAGE IA          0        0        1        0        0
  STAGE IA1         0        0        1        0        0
  STAGE IA2         0        0        1        0        0
  STAGE IB          5        7       13        6        7
  STAGE IB1        26       17       25        1        9
  STAGE IB2         9       12        8        2        8
  STAGE II          1        3        1        0        0
  STAGE IIA         2        1        2        1        3
  STAGE IIA1        1        0        1        1        2
  STAGE IIA2        0        3        1        2        1
  STAGE IIB         5       18        5        5       11
  STAGE III         0        0        0        1        0
  STAGE IIIA        0        3        0        0        0
  STAGE IIIB        6       19       11        3        3
  STAGE IVA         1        5        2        0        1
  STAGE IVB         3        6        1        2        0
[1] 17  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 82 20
  subtype2 59 19
  subtype3 73 30
subtype1 subtype2 subtype3 
     102       78      103 
subtype1 subtype2 subtype3 
      20       19       30 
$subtype1
TCGA-C5-A8XJ TCGA-EK-A2GZ TCGA-EX-A69M TCGA-VS-A9V4 TCGA-ZJ-AAX4 TCGA-2W-A8YY 
      146.86        12.59         8.32         4.34         0.69        17.52 
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2M1 
       31.40        35.01        57.73        35.61        20.91        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7X8 
       33.24        52.01        18.02       210.67        20.35         2.73 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 
        8.35        99.91        27.52         4.90       160.41        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-EA-A410 TCGA-EA-A439 
        1.12        95.11        82.06        16.18        26.40        31.73 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IR 
       24.82        14.89        26.79        27.22        24.00       113.16 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK 
        1.51         0.39         0.89        47.77         1.64         0.49 
TCGA-EK-A3GN TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A40J 
        0.89        15.55        12.23        19.04        36.26        14.01 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VK 
        1.12         9.44       137.16        81.96         3.29        20.48 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3X 
       28.37        18.15        44.61         0.30        13.35        20.28 
TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       19.56        11.38        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.58        15.95        16.14        17.56        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       18.64        22.62        69.50        10.03        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 
       19.96        36.13        39.78        40.14        58.45        55.50 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UJ 
       51.32        50.47        43.40        27.12        24.30         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UV 
       14.53        27.25        47.87        47.47        26.07         3.42 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-ZJ-AAXA 
       67.20        18.84         5.16        17.75        16.24         1.41 

$subtype2
TCGA-FU-A3TX TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1MJ 
        1.48        17.82        23.67        18.74        36.56         0.46 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
        2.43         3.58        44.22        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7XC TCGA-C5-A8YT 
      134.33        15.48       147.35       155.77        50.99        20.81 
TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1O9 
       20.91        17.03        44.94        58.88        36.76         8.75 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       28.90        16.83        17.52        39.55        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E 
       31.53        31.36        13.05        24.56        12.13         7.46 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PM 
       27.29        27.25        13.48         0.36        19.27         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RK TCGA-EK-A2RO TCGA-EX-A1H6 
        1.45         0.13         4.24         0.43         0.07         7.92 
TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-HG-A2PA 
       16.11        20.98        16.14        28.31        35.44        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LB 
       16.57        21.67        20.78        14.93       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MU-A51Y 
      129.37        96.95        11.28         0.89        22.52        28.08 
TCGA-MU-A8JM TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A954 
       19.96        16.41        93.99        11.51        31.27        56.35 
TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZX-AA5X 
       41.52        15.85        18.25        26.01        29.26         3.91 

$subtype3
TCGA-DS-A1OC TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ 
       12.36        49.48        57.04        11.44        68.84       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A1MQ TCGA-C5-A2LT 
       30.21        53.16        38.99        40.93        33.90        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7UC 
       73.45        83.05        78.35       100.14       154.32        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8YQ 
      131.11        94.95         9.34        13.61        45.83        23.51 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OB 
       63.98        87.75        55.63       117.99       118.65        28.31 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HU TCGA-EA-A3QE 
      127.36        22.98         8.28        40.87        33.30        25.02 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       36.89        26.01        60.72        26.27         6.64         0.43 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-EX-A69L 
       40.96         0.30         1.74         0.10        15.22        19.79 
TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-GH-A9DA TCGA-IR-A3LH 
       23.84        31.36        26.14        10.55        17.75        78.71 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       29.85        36.36        27.42        24.56        21.44        15.58 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3Y 
        8.28        21.11        20.91        12.49         0.82        17.82 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V 
        9.17         8.52        17.23         9.04        14.07        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL 
       14.60        11.67        32.42        23.97        27.25        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       32.15        53.59        59.18        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UH 
       33.37        50.14        48.39        28.50        29.95        46.92 
TCGA-VS-A9UI TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       45.11        14.53        18.25        15.42        67.59        19.13 
TCGA-ZJ-AAXU 
        0.16 

subtype1 subtype2 subtype3 
    0.30     0.07     0.10 
subtype1 subtype2 subtype3 
  210.67   155.77   177.04 
subtype1 subtype2 subtype3 
  20.415   20.795   28.500 
[1] "0.3 - 210.7 (20.4)" "0.1 - 155.8 (20.8)" "0.1 - 177.0 (28.5)"
D9V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 44 25 10  5
  subtype2 44 13  3  2
  subtype3 48 30  6  2
D9V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       44       44       48
  T2       25       13       30
  T3       10        3        6
  T4        5        2        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"
D9V4, binary
          cls
clus        0  1
  subtype1 42 14
  subtype2 42 20
  subtype3 46 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   14
  subtype2   42   20
  subtype3   46   23
   clus
vv  subtype1 subtype2 subtype3
  0       42       42       46
  1       14       20       23
[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"
D9V5, binary
          cls
clus        0  1
  subtype1 32  6
  subtype2 36  1
  subtype3 44  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32    6
  subtype2   36    1
  subtype3   44    2
   clus
vv  subtype1 subtype2 subtype3
  0       32       36       44
  1        6        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"
D9V6, binary
          cls
clus        0  1
  subtype1 22 51
  subtype2 12 26
  subtype3 19 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   51
  subtype2   12   26
  subtype3   19   47
     clus
vv    subtype1 subtype2 subtype3
  NO        22       12       19
  YES       51       26       47
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               65
  subtype2             1                               69
  subtype3             0                              108
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             2
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   6
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           13
  subtype2                                            4
  subtype3                                            0
D9V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    65       69      108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        6        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        13        4        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"
D9V8, continuous
D9V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                        13
  subtype2                                1     8                         3
  subtype3                                5     4                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    69
  subtype2                                         0    60
  subtype3                                         2    76
D9V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        5
  ASIAN                                            7        8        4
  BLACK OR AFRICAN AMERICAN                       13        3       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           69       60       76
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
          cls
clus        0  1
  subtype1  8 53
  subtype2  4 52
  subtype3 12 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   53
  subtype2    4   52
  subtype3   12   56
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        4       12
  NOT HISPANIC OR LATINO       53       52       56
[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"
D9V12, continuous
D9V13, binary
          cls
clus        0  1
  subtype1 64 30
  subtype2 55 20
  subtype3 75 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64   30
  subtype2   55   20
  subtype3   75   25
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       64       55       75
  WITH TUMOR       30       20       25
[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       G1 G2 G3 G4 GX
  subtype1  5 37 47  0 13
  subtype2  9 43 29  0  1
  subtype3  2 48 42  1  9
D9V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        5        9        2
  G2       37       43       48
  G3       47       29       42
  G4        0        0        1
  GX       13        1        9
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, continuous
D9V16, continuous
D9V17, continuous
D9V18, continuous
D9V19, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2  6  1
  subtype3 16  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    6    1
  subtype3   16    2
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           5        6       16
  TREATMENT NOT COMPLETED        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"
D9V20, continuous
D9V21, continuous
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       8
  subtype2                                   3                      12
  subtype3                                   3                      19
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       7
  subtype3                       0                       3
D9V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        3
  OTHER LOCATION, SPECIFY                    8       12       19
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        7        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             1
  subtype2                                             0
  subtype3                                             2
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                             15
  subtype2                                              6
  subtype3                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                26
  subtype2                                                                                29
  subtype3                                                                                23
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           39
  subtype2                                                                                           28
  subtype3                                                                                           53
D9V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       39
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       28
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       53
[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"
D9V28, binary
          cls
clus        0  1
  subtype1 20 25
  subtype2 23 26
  subtype3 26 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   25
  subtype2   23   26
  subtype3   26   23
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        20       23       26
  PRESENT       25       26       23
[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"
D9V29, continuous
D9V30, continuous
D9V31, binary
          cls
clus        0  1
  subtype1  5 34
  subtype2 21 30
  subtype3 26 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   34
  subtype2   21   30
  subtype3   26   50
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            5       21       26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       34       30       50
[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"
D9V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          20         33
  subtype2            3          18         19
  subtype3            6          16         33
D9V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        6        3        6
  FORMER USER        20       18       16
  NEVER USED         33       19       33
[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"
D9V34, continuous
D9V35, binary
          cls
clus        0  1
  subtype1 28  6
  subtype2 31  7
  subtype3 36  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    6
  subtype2   31    7
  subtype3   36    6
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        28       31       36
  PRESENT        6        7        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           3        37     1
  subtype2           2        19     0
  subtype3           2        46     1
D9V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        3        2        2
  CISPLATIN         37       19       46
  OTHER              1        0        1
[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"
D9V37, continuous
D9V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       3        0         0        8        29        16        2
  subtype2       0        1         1        7        27        11        2
  subtype3       2        0         0       22        20        10        1
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIA STAGE IIIB
  subtype1         2          1          3        11          2         14
  subtype2         3          1          2         6          0         13
  subtype3         3          3          2        25          1         14
          vv
clus       STAGE IVA STAGE IVB
  subtype1         2         7
  subtype2         4         1
  subtype3         2         3
D9V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        2
  STAGE IA          0        1        0
  STAGE IA2         0        1        0
  STAGE IB          8        7       22
  STAGE IB1        29       27       20
  STAGE IB2        16       11       10
  STAGE II          2        2        1
  STAGE IIA         2        3        3
  STAGE IIA1        1        1        3
  STAGE IIA2        3        2        2
  STAGE IIB        11        6       25
  STAGE IIIA        2        0        1
  STAGE IIIB       14       13       14
  STAGE IVA         2        4        2
  STAGE IVB         7        1        3
[1] 15  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 23  5
  subtype2 58 20
  subtype3 81 24
  subtype4 29 11
  subtype5 23  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       78      105       40       32 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       20       24       11        9 
$subtype1
TCGA-2W-A8YY TCGA-DG-A2KK TCGA-DS-A7WF TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA 
       17.52        82.06        16.18        26.40        31.73        24.82 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A8YF 
       14.89        27.22         0.89         1.64         0.49        15.55 
TCGA-FU-A3HZ TCGA-FU-A57G TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-JW-A5VH TCGA-JX-A3Q8 
       36.26        35.44         9.44       137.16         3.29        44.61 
TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-VS-A8EJ TCGA-VS-A8QA 
       54.81         2.96        16.14        18.64        19.96        36.13 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UR 
        1.71        14.53        47.47        26.07 

$subtype2
TCGA-C5-A8XJ TCGA-FU-A3TX TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE 
      146.86         1.48        17.82        49.48        23.67        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1M7 
       18.74        36.56       144.16       177.04        67.46        46.32 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       38.99         2.43         3.58        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8YT 
       15.48       147.35       155.77         9.34        50.99        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       20.91        44.94        87.75        58.88        36.76        55.63 
TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
        8.75        28.90        16.83        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A50E TCGA-EA-A5FO 
       30.90        31.53        31.36        24.56         7.46        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PM 
       27.29        27.25        13.48         0.36        19.27         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RK TCGA-EK-A2RO TCGA-EK-A3GN 
        1.45         0.13         4.24         0.43         0.07         0.89 
TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HG-A9SC 
       15.22        20.98        16.14        28.31        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-LP-A4AW 
       21.67        20.78        14.93       147.39       129.37         0.89 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MU-A51Y TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PF 
       13.35        22.52        28.08        16.41        19.59        93.99 
TCGA-VS-A8EI TCGA-VS-A8QM TCGA-VS-A9UT TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZX-AA5X 
       23.97        31.27        15.85        18.25        29.26         3.91 

$subtype3
TCGA-DS-A1OC TCGA-EK-A2GZ TCGA-EX-A69M TCGA-ZJ-AAX4 TCGA-BI-A0VS TCGA-C5-A1BL 
       12.36        12.59         8.32         0.69        57.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       82.85        19.86        31.40        30.21        35.01        53.16 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY 
       35.61        20.91        33.90        73.18        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8YQ 
      100.14       210.67       131.11        94.95         8.35        23.51 
TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-DG-A2KM TCGA-DS-A0VN TCGA-DS-A1OB 
       17.03         4.90       160.41        63.98       118.65        28.31 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
      127.36        22.98         8.28        33.30        13.05        25.02 
TCGA-EA-A44S TCGA-EA-A6QX TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2RA TCGA-EK-A2RB 
       12.13        24.00       113.16         1.51        40.96         0.30 
TCGA-EK-A3GJ TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3TQ 
        0.10        19.79        12.23        23.84        19.04        26.14 
TCGA-FU-A5XV TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
       10.55        78.71        81.96        29.85        36.36        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV 
       21.44        20.48        15.58         8.28        18.15        20.91 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.30         0.82        20.28        19.56         9.17         8.52 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       19.96        35.05        20.84        15.95         9.04        17.56 
TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        9.34        22.62        14.60        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EK TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF 
       32.42        27.25        32.15        53.59        11.51        59.18 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.87        16.64        33.37        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UD 
       51.32        50.47        43.40        48.39        27.12        24.30 
TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 
       45.11        27.25        14.53         3.42        18.25        17.75 
TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01         1.41         0.16 

$subtype4
TCGA-C5-A0TN TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC 
       11.44        40.93        73.45        52.01       154.32        17.19 
TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DS-A0VM 
       13.61        45.83        99.91        27.52        14.73       117.99 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK 
       36.89        26.01        60.72        26.27         6.64         0.39 
TCGA-EK-A2PL TCGA-EK-A2RJ TCGA-FU-A3HY TCGA-GH-A9DA TCGA-JW-A5VG TCGA-JX-A3PZ 
        0.43         1.74        31.36        17.75        27.42        21.11 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MY-A913 TCGA-Q1-A73O 
       11.28        12.49        17.82        11.38        17.23        14.07 
TCGA-UC-A7PD TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A9UA TCGA-VS-A9UB 
       11.67        65.49         4.73        40.14        28.50        29.95 
TCGA-VS-A9UH TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       46.92        15.42        67.59        19.13 

$subtype5
TCGA-VS-A9V4 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
        4.34        57.73         0.46        44.22        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-DG-A2KH TCGA-DG-A2KJ 
       18.02        17.85        20.35         2.73         1.12        95.11 
TCGA-DS-A7WH TCGA-EK-A2RL TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A770 
       17.52        47.77         7.92        16.11        14.01         1.12 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JW-A69B TCGA-Q1-A5R1 TCGA-Q1-A73P TCGA-UC-A7PI 
       66.81        96.95        28.37        15.58        15.88        69.50 
TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UZ TCGA-VS-A9V0 
       39.78        58.45        47.87        41.52        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V5 
        5.16        16.24 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.49     0.07     0.10     0.39     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
  137.16   177.04   210.67   154.32    96.95 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.300   23.820   24.300   23.560   19.595 
[1] "0.5 - 137.2 (19.3)" "0.1 - 177.0 (23.8)" "0.1 - 210.7 (24.3)"
[4] "0.4 - 154.3 (23.6)" "0.5 - 97.0 (19.6)" 
D10V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 13 12  1  1
  subtype2 42 13  3  2
  subtype3 43 31 10  4
  subtype4 18  6  4  1
  subtype5 20  6  1  1
D10V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       13       42       43       18       20
  T2       12       13       31        6        6
  T3        1        3       10        4        1
  T4        1        2        4        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"
D10V4, binary
          cls
clus        0  1
  subtype1 18  2
  subtype2 42 17
  subtype3 37 26
  subtype4 15  7
  subtype5 18  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    2
  subtype2   42   17
  subtype3   37   26
  subtype4   15    7
  subtype5   18    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       18       42       37       15       18
  1        2       17       26        7        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 15  3
  subtype2 40  1
  subtype3 35  4
  subtype4 14  1
  subtype5  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    3
  subtype2   40    1
  subtype3   35    4
  subtype4   14    1
  subtype5    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       15       40       35       14        8
  1        3        1        4        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"
D10V6, binary
          cls
clus        0  1
  subtype1  7 14
  subtype2 11 23
  subtype3 19 53
  subtype4  9 19
  subtype5  7 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   14
  subtype2   11   23
  subtype3   19   53
  subtype4    9   19
  subtype5    7   15
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7       11       19        9        7
  YES       14       23       53       19       15
[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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               15
  subtype2             1                               78
  subtype3             1                              105
  subtype4             0                               42
  subtype5             1                                2
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             0
  subtype3                                             1
  subtype4                                             0
  subtype5                                             4
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   5
  subtype2                                   1
  subtype3                                   2
  subtype4                                   0
  subtype5                                  12
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         1
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            3
  subtype2                                            1
  subtype3                                            0
  subtype4                                            0
  subtype5                                           13
D10V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        1        1
  CERVICAL SQUAMOUS CELL CARCINOMA                    15       78      105
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        0        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  5        1        2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         3        1        0
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        1
  CERVICAL SQUAMOUS CELL CARCINOMA                    42        2
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0       12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0       13
[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"
D10V8, continuous
D10V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         2
  subtype2                                1     9                         4
  subtype3                                3     4                        13
  subtype4                                2     2                         7
  subtype5                                0     0                         1
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    17
  subtype2                                         0    59
  subtype3                                         1    74
  subtype4                                         1    27
  subtype5                                         0    28
D10V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        3        2
  ASIAN                                            4        9        4        2
  BLACK OR AFRICAN AMERICAN                        2        4       13        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1        1
  WHITE                                           17       59       74       27
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 0
  ASIAN                                            0
  BLACK OR AFRICAN AMERICAN                        1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           28
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
          cls
clus        0  1
  subtype1  3 16
  subtype2  3 55
  subtype3 10 52
  subtype4  5 22
  subtype5  3 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   16
  subtype2    3   55
  subtype3   10   52
  subtype4    5   22
  subtype5    3   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        3       10        5        3
  NOT HISPANIC OR LATINO       16       55       52       22       16
[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"
D10V12, continuous
D10V13, binary
          cls
clus        0  1
  subtype1 17 11
  subtype2 54 21
  subtype3 73 27
  subtype4 29  8
  subtype5 21  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   11
  subtype2   54   21
  subtype3   73   27
  subtype4   29    8
  subtype5   21    8
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       17       54       73       29       21
  WITH TUMOR       11       21       27        8        8
[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       G1 G2 G3 G4 GX
  subtype1  1  6 18  0  4
  subtype2  7 39 32  0  2
  subtype3  3 52 39  1 10
  subtype4  0 10 24  0  5
  subtype5  5 21  5  0  2
D10V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        1        7        3        0        5
  G2        6       39       52       10       21
  G3       18       32       39       24        5
  G4        0        0        1        0        0
  GX        4        2       10        5        2
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        9       18        6        6 
 [1] "subtype3" "subtype2" "subtype5" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype5" "subtype3" "subtype2" "subtype5"
[13] "subtype4" "subtype5" "subtype2" "subtype4" "subtype4" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype5" "subtype3" "subtype4" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype5" "subtype3" "subtype4"
[37] "subtype3" "subtype4" "subtype3"
D10V16, continuous
D10V17, continuous
D10V18, continuous
D10V19, binary
          cls
clus        0  1
  subtype1  0  0
  subtype2  8  1
  subtype3 16  0
  subtype4  2  2
  subtype5  1  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    0
  subtype2    8    1
  subtype3   16    0
  subtype4    2    2
  subtype5    1    0
                         clus
vv                        subtype2 subtype3 subtype4 subtype5
  COMPLETED AS PLANNED           8       16        2        1
  TREATMENT NOT COMPLETED        1        0        2        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V20, continuous
D10V21, continuous
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       1
  subtype2                                   1                      15
  subtype3                                   5                      12
  subtype4                                   1                       5
  subtype5                                   0                       6
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       1                       5
  subtype3                       0                       5
  subtype4                       0                       0
  subtype5                       0                       1
D10V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0        1        5        1
  OTHER LOCATION, SPECIFY                    1       15       12        5
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    1        5        5        0
                                     clus
vv                                    subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0
  OTHER LOCATION, SPECIFY                    6
  POSITIVE BLADDER MARGIN                    0
  POSITIVE VAGINAL MARGIN                    1
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             1
  subtype4                                             1
  subtype5                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              3
  subtype2                                              5
  subtype3                                             11
  subtype4                                              3
  subtype5                                              3
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 6
  subtype2                                                                                29
  subtype3                                                                                30
  subtype4                                                                                 4
  subtype5                                                                                 9
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           16
  subtype2                                                                                           27
  subtype3                                                                                           43
  subtype4                                                                                           19
  subtype5                                                                                           15
D10V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       43
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       19
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       15
[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"
D10V28, binary
          cls
clus        0  1
  subtype1  6 12
  subtype2 25 27
  subtype3 19 25
  subtype4  6  6
  subtype5 13  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   12
  subtype2   25   27
  subtype3   19   25
  subtype4    6    6
  subtype5   13    4
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT         6       25       19        6       13
  PRESENT       12       27       25        6        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"
D10V29, continuous
D10V30, continuous
D10V31, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2 23 35
  subtype3 19 46
  subtype4 10 19
  subtype5  0  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2   23   35
  subtype3   19   46
  subtype4   10   19
  subtype5    0    4
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       23       19       10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       10       35       46       19
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA            0
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        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"
D10V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            4           6          8
  subtype2            2          13         22
  subtype3            4          21         35
  subtype4            2           6         11
  subtype5            3           8          9
D10V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        4        2        4        2        3
  FORMER USER         6       13       21        6        8
  NEVER USED          8       22       35       11        9
[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"
D10V34, continuous
D10V35, binary
          cls
clus        0  1
  subtype1 10  4
  subtype2 34  9
  subtype3 28  5
  subtype4  8  0
  subtype5 15  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    4
  subtype2   34    9
  subtype3   28    5
  subtype4    8    0
  subtype5   15    1
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        10       34       28        8       15
  PRESENT        4        9        5        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           2         9     0
  subtype2           2        19     0
  subtype3           1        48     0
  subtype4           1        16     1
  subtype5           1        10     1
D10V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        2        2        1        1        1
  CISPLATIN          9       19       48       16       10
  OTHER              0        0        0        1        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        7        5        3 
 [1] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype4"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype4" "subtype2"
D10V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       1        0         0        2         8         5        0
  subtype2       0        1         1       14        22         9        3
  subtype3       3        0         0       11        24        10        2
  subtype4       1        0         0        7         7         7        0
  subtype5       0        0         0        3        15         6        0
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIA STAGE IIIB
  subtype1         2          1          2         4          0          2
  subtype2         2          2          2         7          0         13
  subtype3         1          2          3        20          1         18
  subtype4         2          0          0         8          2          5
  subtype5         1          0          0         3          0          3
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         2
  subtype2         3         1
  subtype3         3         6
  subtype4         1         1
  subtype5         1         1
D10V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        3        1        0
  STAGE IA          0        1        0        0        0
  STAGE IA2         0        1        0        0        0
  STAGE IB          2       14       11        7        3
  STAGE IB1         8       22       24        7       15
  STAGE IB2         5        9       10        7        6
  STAGE II          0        3        2        0        0
  STAGE IIA         2        2        1        2        1
  STAGE IIA1        1        2        2        0        0
  STAGE IIA2        2        2        3        0        0
  STAGE IIB         4        7       20        8        3
  STAGE IIIA        0        0        1        2        0
  STAGE IIIB        2       13       18        5        3
  STAGE IVA         0        3        3        1        1
  STAGE IVB         2        1        6        1        1
[1] 15  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
