[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/15076797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/15095897/CESC-TP.mergedcluster.txt"

nPatients in clinical file=304, in cluster file=307, common to both=304
[1]  10 304
[1] "CN_CNMF"
[1] 3
  1   2   3 
128  71  93 
  1   2   3 
128  71  93 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6 
70 58 59 61 11 45 
 1  2  3  4  5  6 
70 58 59 61 11 45 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
52 46 74 
 1  2  3 
52 46 74 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
31 49 51 23 18 
 1  2  3  4  5 
31 49 51 23 18 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
 56 104  69  72 
  1   2   3   4 
 56 104  69  72 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 70 194  37 
  1   2   3 
 70 194  37 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
102  79 123 
  1   2   3 
102  79 123 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 58 101  74  26  45 
  1   2   3   4   5 
 58 101  74  26  45 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
127  77  87 
  1   2   3 
127  77  87 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 62  50  31 148 
  1   2   3   4 
 62  50  31 148 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                  
 [2] "VITAL_STATUS"                                    
 [3] "DAYS_TO_DEATH"                                   
 [4] "DAYS_TO_LAST_FOLLOWUP"                           
 [5] "PRIMARY_SITE_OF_DISEASE"                         
 [6] "NEOPLASM_DISEASESTAGE"                           
 [7] "PATHOLOGY_T_STAGE"                               
 [8] "PATHOLOGY_N_STAGE"                               
 [9] "PATHOLOGY_M_STAGE"                               
[10] "DCC_UPLOAD_DATE"                                 
[11] "GENDER"                                          
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"            
[13] "HISTOLOGICAL_TYPE"                               
[14] "RADIATIONS_RADIATION_REGIMENINDICATION"          
[15] "NUMBER_PACK_YEARS_SMOKED"                        
[16] "NUMBER_OF_LYMPH_NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCH_NUMBER"                                    
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASM_HISTOLOGIC_GRADE"                       
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "LYMPH_NODE_LOCATION"                             
[42] "POS_LYMPH_NODE_LOCATION"                         
[43] "MENOPAUSE_STATUS"                                
[44] "LYMPHOVASCULAR_INVOLVEMENT"                      
[45] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[46] "LYMPH_NODES_EXAMINED"                            
[47] "KERATINIZATION_SQUAMOUS_CELL"                    
[48] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[49] "HYSTERECTOMY_TYPE"                               
[50] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[51] "HEIGHT_CM_AT_DIAGNOSIS"                          
[52] "FEDPET_OR_CT_RESULTS"                            
[53] "CORPUS_INVOLVEMENT"                              
[54] "CHEMO_CONCURRENT_TYPE"                           
[55] "CERVIX_SUV_RESULTS"                              
[56] "CAUSE_OF_DEATH"                                  
[57] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[58] "AGE_AT_DIAGNOSIS"                                
[59] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 59 rows and 304 columns.

[1] "Batch" "19"   
[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=67,	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=211,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE 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:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'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 12:'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 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH_NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_TREATMENT_ADJUVANT is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT 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 EXTENTION 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 41:'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 42:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'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 50:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 51:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 52:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "FEDPET_OR_CT_RESULTS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 53:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 56:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 57:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 58:'AGE_AT_DIAGNOSIS':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 59:'STAGE_EVENT.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 304 columns, 1 survival variables, and 44 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] "HISTOLOGICAL_TYPE"                               
 [6] "RADIATIONS_RADIATION_REGIMENINDICATION"          
 [7] "NUMBER_PACK_YEARS_SMOKED"                        
 [8] "NUMBER_OF_LYMPH_NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASM_HISTOLOGIC_GRADE"                       
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CHEMO_CONCURRENT_TYPE"                           
[41] "CERVIX_SUV_RESULTS"                              
[42] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[43] "AGE_AT_DIAGNOSIS"                                
[44] "STAGE_EVENT.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 
140  70  21  10 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
140  70  21  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
140  70  21  10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
140  70  21  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, 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
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=7, 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=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=28, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=43, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=15, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, 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=36, 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
AJCC_TUMOR_PATHOLOGIC_PT, nv=15, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=62, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=17, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1 100  25
  subtype2  44  20
  subtype3  69  20
subtype1 subtype2 subtype3 
     125       64       89 
subtype1 subtype2 subtype3 
      25       20       20 
$subtype1
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ 
       18.74        36.56       144.16       177.04        82.85        19.86 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       46.32        35.01        38.99         0.46         2.43         3.58 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       38.43        18.02        17.85        20.42       210.67       101.82 
TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ 
       17.19        94.95         9.34       146.86        20.81        20.91 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A5RQ 
        1.12        44.94        40.04        58.88       118.65        16.83 
TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       16.18        39.55        13.05        25.02        14.50        26.40 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A6QX TCGA-EK-A2H1 
       12.66        12.82         7.46        26.79        13.58        26.27 
TCGA-EK-A2IP TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A3GJ 
        6.64         1.45         0.07         4.04         0.36         0.10 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K 
        0.10         7.92         6.94        14.70        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36        36.26         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        0.82         3.52         1.32         1.12         9.01        25.41 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       20.78         9.44       147.39       137.16        66.81        96.95 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
       28.37       195.85        30.31        11.28        12.49         0.30 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI 
       17.82        19.56         9.17         8.52        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73O 
        5.42        35.05        20.84        15.58        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI 
       15.88        15.39        19.59         3.88        11.67        66.05 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 
       59.51        46.03        39.78        31.27        24.39        50.86 
TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UJ 
       50.14        42.41        25.74        21.30        46.92         1.71 
TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       20.09        14.53        67.20         5.16        14.04        14.89 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZX-AA5X 
       16.24        15.42        29.26         0.69         3.91 

$subtype2
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1ME TCGA-C5-A1MI 
       12.39        23.67        11.44         5.46        57.73        35.61 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CM TCGA-C5-A7CO 
       40.93        73.18        73.45        52.01        20.35       147.35 
TCGA-C5-A7UH TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 
      131.11        50.99        45.83        99.91        27.52        11.87 
TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A411 TCGA-EA-A439 
       58.88       117.99        17.52         8.28        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.01        14.89        45.96         0.43         0.59         0.59 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A23L TCGA-FU-A40J 
       16.08         1.18         2.24         0.10        23.84         1.35 
TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JX-A3PZ 
        1.97        10.82        21.67        78.71        29.85        21.11 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-UC-A7PG 
       11.38         5.49         2.96         9.04        19.36        12.16 
TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y 
       10.03        18.05        19.96        57.93        16.64         4.73 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UY 
       45.34        44.94        22.72        40.96        14.53        18.25 
TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       18.84         4.34        67.59        19.13 

$subtype3
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M6 
       49.48        57.04        68.84       173.29        67.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
       30.21        53.16        20.91        44.22        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE 
      100.14        33.24       154.32       134.33        15.48       155.77 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KK TCGA-DR-A0ZL 
       13.61         2.73         8.35        23.51        50.76        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       36.76         2.66        22.98        12.36        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       31.53        31.36        13.91        15.02        14.99        14.96 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2R9 
       13.48         0.36        12.59         1.51        19.27         0.13 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A69L 
        0.03        47.77         0.07         0.03        20.35        19.79 
TCGA-EX-A69M TCGA-FU-A3NI TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LI TCGA-JW-A5VK 
        8.32         1.45        14.93       117.40        81.96        20.48 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU 
        8.28        18.15         7.99         0.89         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW 
       22.52        20.28        54.81        16.41        15.95        17.56 
TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 
        9.34        93.99        40.50        37.78        26.43        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A94W TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 
       36.13        11.51        36.26        39.78        15.68        50.63 
TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       48.07        43.40        19.69        27.25        41.42        43.27 
TCGA-VS-A9UQ TCGA-VS-A9UV TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       35.97         3.42        26.01         1.41         0.16 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  210.67   147.35   173.29 
subtype1 subtype2 subtype3 
  17.850   19.245   22.980 
[1] "0.1 - 210.7 (17.9)" "0.1 - 147.3 (19.2)" "0.0 - 173.3 (23.0)"
D1V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 61 36  5  4
  subtype2 29 17  6  1
  subtype3 44 15 10  3
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       61       29       44
  T2       36       17       15
  T3        5        6       10
  T4        4        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"
D1V4, binary
          cls
clus        0  1
  subtype1 66 21
  subtype2 24 16
  subtype3 37 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   21
  subtype2   24   16
  subtype3   37   18
   clus
vv  subtype1 subtype2 subtype3
  0       66       24       37
  1       21       16       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 43  5
  subtype2 23  3
  subtype3 41  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    5
  subtype2   23    3
  subtype3   41    2
   clus
vv  subtype1 subtype2 subtype3
  0       43       23       41
  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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               97
  subtype2             2                               60
  subtype3             0                               84
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             3
  subtype2                                             2
  subtype3                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   4
  subtype3                                   4
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         1
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            9
  subtype2                                            2
  subtype3                                            4
D1V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    97       60       84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        3        2        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        4        4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        1        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         9        2        4
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  12 116
  subtype2   8  63
  subtype3  10  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  116
  subtype2    8   63
  subtype3   10   83
     clus
vv    subtype1 subtype2 subtype3
  NO        12        8       10
  YES      116       63       83
[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"
D1V8, continuous
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                6     7                        11
  subtype2                                0     1                         8
  subtype3                                2    10                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    90
  subtype2                                         1    54
  subtype3                                         0    57
D1V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 6        0        2
  ASIAN                                            7        1       10
  BLACK OR AFRICAN AMERICAN                       11        8        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        1        0
  WHITE                                           90       54       57
[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"
D1V11, binary
          cls
clus        0  1
  subtype1 13 70
  subtype2  5 40
  subtype3  5 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   70
  subtype2    5   40
  subtype3    5   51
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        5        5
  NOT HISPANIC OR LATINO       70       40       51
[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"
D1V12, continuous
D1V13, binary
          cls
clus        0  1
  subtype1 61 17
  subtype2 29 11
  subtype3 44 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   17
  subtype2   29   11
  subtype3   44   13
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       61       29       44
  WITH TUMOR       17       11       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"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     21      3       0      3       4            92       5
  subtype2     14      1       1      3       1            50       1
  subtype3     18      1       0      5       2            59       8
D1V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              21       14       18
  CANADA               3        1        1
  NIGERIA              0        1        0
  RUSSIA               3        3        5
  UKRAINE              4        1        2
  UNITED STATES       92       50       59
  VIETNAM              5        1        8
[1] 7 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 10 58 48  0 10
  subtype2  2 20 36  1  7
  subtype3  6 51 29  0  7
D1V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1       10        2        6
  G2       58       20       51
  G3       48       36       29
  G4        0        1        0
  GX       10        7        7
[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"
D1V16, continuous
D1V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          15
  subtype2                                          13
  subtype3                                           9
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      3
  subtype2                                      1
  subtype3                                      5
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             27
  subtype2                                               1             14
  subtype3                                               1             21
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  71
  subtype2                  27
  subtype3                  44
D1V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           15       13        9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 3        1        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        1        1
  CURRENT SMOKER                                        27       14       21
  LIFELONG NON-SMOKER                                   71       27       44
[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"
D1V19, continuous
D1V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           7       45             5       12
  subtype2           4       26             4        6
  subtype3           8       31             3        7
D1V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          7        4        8
  EXTERNAL            45       26       31
  EXTERNAL BEAM        5        4        3
  INTERNAL            12        6        7
[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"
D1V22, binary
          cls
clus        0  1
  subtype1  9  1
  subtype2  6  2
  subtype3 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2    6    2
  subtype3   10    0
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           9        6       10
  TREATMENT NOT COMPLETED        1        2        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  2                0                  15
  subtype2                  0                2                  11
  subtype3                  0                0                  10
          vv
clus       REGIONAL SITE
  subtype1            12
  subtype2             8
  subtype3            13
D1V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         2        0        0
  LOCAL RECURRENCE           0        2        0
  PRIMARY TUMOR FIELD       15       11       10
  REGIONAL SITE             12        8       13
[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"
D1V24, binary
          cls
clus        0  1
  subtype1 22  2
  subtype2 17  2
  subtype3 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    2
  subtype2   17    2
  subtype3   17    1
     clus
vv    subtype1 subtype2 subtype3
  CGY       22       17       17
  GY         2        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"
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                      17
  subtype2                                   3                       7
  subtype3                                   3                      11
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       4
  subtype2                       0                       1
  subtype3                       0                       3
D1V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        3
  OTHER LOCATION, SPECIFY                   17        7       11
  POSITIVE BLADDER MARGIN                    1        0        0
  POSITIVE VAGINAL MARGIN                    4        1        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                                             0
  subtype3                                             2
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              7
  subtype2                                              4
  subtype3                                             14
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                33
  subtype2                                                                                16
  subtype3                                                                                32
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           62
  subtype2                                                                                           30
  subtype3                                                                                           28
D1V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       62
                                                                                              clus
vv                                                                                             subtype2
  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)                  16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     14
  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)       28
[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"
D1V33, binary
          cls
clus        0  1
  subtype1 39 32
  subtype2  9 19
  subtype3 22 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   32
  subtype2    9   19
  subtype3   22   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        39        9       22
  PRESENT       32       19       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"
D1V34, continuous
D1V35, continuous
D1V36, binary
          cls
clus        0  1
  subtype1 21 50
  subtype2 10 27
  subtype3 17 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   50
  subtype2   10   27
  subtype3   17   39
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           21       10       17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       50       27       39
[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"
D1V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            9          27         33
  subtype2            3          12         19
  subtype3            3          14         32
D1V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        9        3        3
  FORMER USER        27       12       14
  NEVER USED         33       19       32
[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"
D1V39, continuous
D1V40, binary
          cls
clus        0  1
  subtype1 46  6
  subtype2 15  5
  subtype3 31  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    6
  subtype2   15    5
  subtype3   31    6
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        46       15       31
  PRESENT        6        5        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           1         4     1
  subtype2           0         7     0
  subtype3           0         4     0
D1V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        1        0        0
  CISPLATIN          4        7        4
  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"
D1V42, continuous
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    1  15   31   14  4   6    3    7  16  2   0   3  4   0  7
  subtype2    0   8   13    8  0   0    4    2  11  0   0   6  1   1  3
  subtype3    0  11   25    8  2   4    0    0   9  0   2   8  3   0  6
D1V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A1        1        0        0
  T1B        15        8       11
  T1B1       31       13       25
  T1B2       14        8        8
  T2          4        0        2
  T2A         6        0        4
  T2A1        3        4        0
  T2A2        7        2        0
  T2B        16       11        9
  T3          2        0        0
  T3A         0        0        2
  T3B         3        6        8
  T4          4        1        3
  TIS         0        1        0
  TX          7        3        6
[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"
D1V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         1         0       12        40        16
  subtype2       2        0         0         1        8        13        10
  subtype3       2        1         0         0       13        24        10
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         5          2          5        17         1
  subtype2        0         2          3          2        16         0
  subtype3        3         1          0          0        10         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          1         16         2         7
  subtype2          0         11         1         1
  subtype3          2         15         4         4
D1V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        2        2
  STAGE IA          0        0        1
  STAGE IA1         1        0        0
  STAGE IA2         0        1        0
  STAGE IB         12        8       13
  STAGE IB1        40       13       24
  STAGE IB2        16       10       10
  STAGE II          1        0        3
  STAGE IIA         5        2        1
  STAGE IIA1        2        3        0
  STAGE IIA2        5        2        0
  STAGE IIB        17       16       10
  STAGE III         1        0        0
  STAGE IIIA        1        0        2
  STAGE IIIB       16       11       15
  STAGE IVA         2        1        4
  STAGE IVB         7        1        4
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 52 16
  subtype2 44 12
  subtype3 45 11
  subtype4 35 21
  subtype5  9  1
  subtype6 36  8
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      68       56       56       56       10       44 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      16       12       11       21        1        8 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS 
       31.40        35.01        57.73        35.61         0.46        44.22 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 
       38.43        33.24        18.02        17.85        20.35         2.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 
        1.12        58.88        50.76        16.18        17.52        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2R7 
       24.56        14.50        12.82        14.89        14.96         0.59 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23K 
       47.77         2.24         0.10         7.92        14.70         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A9SC 
        2.17        36.26         1.35         1.32         1.12        10.82 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH 
        9.44       137.16        66.81        96.95        81.96         3.29 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BD TCGA-PN-A8MA 
       28.37        30.31        13.35        11.38        54.81         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI 
       15.58        16.14        15.88        15.39        19.36        66.05 
TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL 
       19.96        36.13        39.78        50.86         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 
       41.42        43.27        35.97        20.09        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V5 
        5.16        16.24 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A7CO 
       12.39       173.29        67.46        83.05       100.14       147.35 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A901 TCGA-C5-A905 TCGA-DS-A0VM TCGA-DS-A1OA 
      131.11        94.95        17.03       160.41       117.99        28.90 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A6QX 
       12.36        37.35        13.05        12.66        26.79        13.58 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-FU-A2QG 
        6.64         1.51        16.08         0.07         4.04         0.92 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK 
       31.36         1.58         1.97       147.39       117.40        29.85 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-LP-A5U3 TCGA-MA-AA3X 
       20.48        15.58        18.15       195.85         0.82        20.28 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-Q1-A5R2 TCGA-UC-A7PG TCGA-VS-A8EK TCGA-VS-A8QC 
        9.17         8.52        16.41        12.16        27.25        11.51 
TCGA-VS-A8QF TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U5 TCGA-VS-A9U7 
       57.93        39.78        15.68        50.63        44.94        42.41 
TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 
       40.96        27.25         3.42        18.25        14.04        14.89 
TCGA-WL-A834 TCGA-ZJ-AAXA 
       26.01         1.41 

$subtype3
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ 
       49.48        36.56       144.16       177.04        82.85        19.86 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A7CG TCGA-C5-A7CJ 
       46.32        38.99         2.43         3.58       210.67       101.82 
TCGA-C5-A7XC TCGA-C5-A8YT TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A1O9 
       50.99        20.81        40.04        87.75        58.88         8.75 
TCGA-DS-A1OD TCGA-EA-A1QS TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A5ZD TCGA-EA-A78R 
      127.36        39.55        33.30        25.02        15.02        13.48 
TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-EX-A69L 
       26.27         1.45         0.03         0.10         6.94        19.79 
TCGA-EX-A8YF TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AU 
       15.55         3.52        21.67        14.93        36.36        11.28 
TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MU-A51Y TCGA-MY-A5BE TCGA-Q1-A73O 
        0.89        22.52        17.82        13.87        35.05        14.07 
TCGA-R2-A69V TCGA-VS-A8EI TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A958 
       19.59        18.05        31.27        36.26        24.39        50.14 
TCGA-VS-A959 TCGA-VS-A9UH TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-XS-A8TJ 
       45.34        46.92        14.53         4.34        15.42        29.26 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

$subtype4
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A1MQ 
       57.04        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-A7CL 
       73.18        73.45        78.35        52.01       154.32        15.48 
TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ 
       17.19         9.34        13.61        45.83        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A907 TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A7WI TCGA-EA-A3Y4 
       27.52        11.87       118.65        12.36         8.28        14.50 
TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2RE 
       26.01         7.46        13.91        45.96         0.43         0.36 
TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-GH-A9DA TCGA-IR-A3LH TCGA-JW-A5VG 
        1.18         0.10         0.03         9.01        78.71        27.42 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-Q1-A6DT 
       24.56        21.44        21.11        12.49         5.49         9.04 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       11.67        10.03        26.43        59.51        32.15        46.03 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       16.64         4.73        25.74        21.30        22.72        19.69 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       67.59        19.13 

$subtype5
TCGA-BI-A20A TCGA-C5-A7UE TCGA-C5-A8ZZ TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-EK-A2IR 
       23.67       155.77        20.91        28.31        22.98       113.16 
TCGA-EK-A2PM TCGA-FU-A23L TCGA-Q1-A73Q TCGA-VS-A8EC 
        0.59        23.84         9.34        40.50 

$subtype6
TCGA-C5-A1BE TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML TCGA-C5-A3HL TCGA-C5-A7CK 
       68.84        30.21        53.16        20.91        20.42       134.33 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A902 TCGA-DG-A2KL TCGA-DS-A0VK TCGA-DS-A0VL 
        8.35       146.86         4.90        44.94        36.76         2.66 
TCGA-DS-A5RQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A5ZE TCGA-EA-A97N 
       16.83        30.90        31.53        31.36        14.99         0.36 
TCGA-EK-A2GZ TCGA-EK-A2PI TCGA-EK-A2R9 TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A69M 
       12.59        19.27         0.13         0.07        20.35         8.32 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-HG-A2PA TCGA-HM-A3JK TCGA-JW-A852 
        1.45         1.48         0.82        25.41        20.78         8.28 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-MA-AA3Z TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF 
        7.99         0.30        19.56        34.62         5.42        20.84 
TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EG TCGA-VS-A957 
       15.95        17.56         3.88        93.99        37.78        48.07 
TCGA-VS-A9U6 TCGA-ZJ-AAX4 
       43.40         0.69 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.07     0.03     0.03     0.59     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  137.16   195.85   210.67   154.32   155.77   146.86 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  17.935   19.265   22.095   20.400   23.755   19.415 
[1] "0.1 - 137.2 (17.9)" "0.1 - 195.8 (19.3)" "0.0 - 210.7 (22.1)"
[4] "0.0 - 154.3 (20.4)" "0.6 - 155.8 (23.8)" "0.1 - 146.9 (19.4)"
D2V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 38 19  4  1
  subtype2 26 10  6  4
  subtype3 25 18  3  3
  subtype4 23 13  5  1
  subtype5  4  1  2  0
  subtype6 24  9  1  1
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       38       26       25       23        4       24
  T2       19       10       18       13        1        9
  T3        4        6        3        5        2        1
  T4        1        4        3        1        0        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus        0  1
  subtype1 37 12
  subtype2 19 14
  subtype3 25 15
  subtype4 25  8
  subtype5  4  2
  subtype6 23  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   12
  subtype2   19   14
  subtype3   25   15
  subtype4   25    8
  subtype5    4    2
  subtype6   23    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       37       19       25       25        4       23
  1       12       14       15        8        2        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 25  5
  subtype2 20  1
  subtype3 27  1
  subtype4 22  2
  subtype5  4  0
  subtype6 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    5
  subtype2   20    1
  subtype3   27    1
  subtype4   22    2
  subtype5    4    0
  subtype6   17    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       25       20       27       22        4       17
  1        5        1        1        2        0        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               21
  subtype2             0                               58
  subtype3             0                               58
  subtype4             0                               61
  subtype5             0                               11
  subtype6             0                               44
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
  subtype6                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  22
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
  subtype6                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           14
  subtype2                                            0
  subtype3                                            1
  subtype4                                            0
  subtype5                                            0
  subtype6                                            0
D2V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    21       58       58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 22        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        14        0        1
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    61       11       44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0        0
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  4 66
  subtype2  3 55
  subtype3  8 51
  subtype4 11 50
  subtype5  2  9
  subtype6  7 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   66
  subtype2    3   55
  subtype3    8   51
  subtype4   11   50
  subtype5    2    9
  subtype6    7   38
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         4        3        8       11        2        7
  YES       66       55       51       50        9       38
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                1     3                         7
  subtype3                                1     6                         7
  subtype4                                4     3                         8
  subtype5                                0     0                         0
  subtype6                                1     2                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    52
  subtype2                                         0    38
  subtype3                                         0    37
  subtype4                                         2    41
  subtype5                                         0    10
  subtype6                                         0    32
D2V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        1        4
  ASIAN                                            5        3        6        3
  BLACK OR AFRICAN AMERICAN                        3        7        7        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           52       38       37       41
                                           clus
vv                                          subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1
  ASIAN                                            0        2
  BLACK OR AFRICAN AMERICAN                        0        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0
  WHITE                                           10       32
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
          cls
clus        0  1
  subtype1  7 38
  subtype2  5 29
  subtype3  4 34
  subtype4  5 35
  subtype5  0  5
  subtype6  3 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   38
  subtype2    5   29
  subtype3    4   34
  subtype4    5   35
  subtype5    0    5
  subtype6    3   28
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            7        5        4        5        0        3
  NOT HISPANIC OR LATINO       38       29       34       35        5       28
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
D2V13, binary
          cls
clus        0  1
  subtype1 34 11
  subtype2 27  8
  subtype3 31  7
  subtype4 23  9
  subtype5  5  2
  subtype6 19  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   11
  subtype2   27    8
  subtype3   31    7
  subtype4   23    9
  subtype5    5    2
  subtype6   19    7
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  TUMOR FREE       34       27       31       23        5       19
  WITH TUMOR       11        8        7        9        2        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     14      3       1      3       1            45       3
  subtype2     14      0       0      3       2            37       2
  subtype3     11      1       0      3       0            40       4
  subtype4     11      0       0      0       3            44       3
  subtype5      1      0       0      0       0            10       0
  subtype6      3      1       0      3       1            35       2
D2V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  BRAZIL              14       14       11       11        1        3
  CANADA               3        0        1        0        0        1
  NIGERIA              1        0        0        0        0        0
  RUSSIA               3        3        3        0        0        3
  UKRAINE              1        2        0        3        0        1
  UNITED STATES       45       37       40       44       10       35
  VIETNAM              3        2        4        3        0        2
[1] 7 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  7 30 27  0  6
  subtype2  2 27 25  0  3
  subtype3  3 29 22  0  4
  subtype4  1 26 24  1  5
  subtype5  0  4  6  0  1
  subtype6  5 20 14  0  5
D2V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  G1        7        2        3        1        0        5
  G2       30       27       29       26        4       20
  G3       27       25       22       24        6       14
  G4        0        0        0        1        0        0
  GX        6        3        4        5        1        5
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V16, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8        9        7        7        1       10 
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype6"
 [7] "subtype3" "subtype1" "subtype4" "subtype1" "subtype2" "subtype4"
[13] "subtype4" "subtype1" "subtype2" "subtype6" "subtype2" "subtype6"
[19] "subtype6" "subtype6" "subtype3" "subtype2" "subtype1" "subtype4"
[25] "subtype2" "subtype1" "subtype6" "subtype6" "subtype6" "subtype1"
[31] "subtype6" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[37] "subtype4" "subtype6" "subtype2" "subtype4" "subtype4"
D2V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           8
  subtype2                                           7
  subtype3                                           7
  subtype4                                           7
  subtype5                                           0
  subtype6                                          10
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      3
  subtype3                                      2
  subtype4                                      0
  subtype5                                      1
  subtype6                                      2
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             11
  subtype2                                               1             12
  subtype3                                               1             12
  subtype4                                               1             17
  subtype5                                               0              3
  subtype6                                               1              9
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  43
  subtype2                  28
  subtype3                  29
  subtype4                  26
  subtype5                   1
  subtype6                  18
D2V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            8        7        7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        3        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        1
  CURRENT SMOKER                                        11       12       12
  LIFELONG NON-SMOKER                                   43       28       29
                                                 clus
vv                                                subtype4 subtype5 subtype6
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        0       10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        1        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0        1
  CURRENT SMOKER                                        17        3        9
  LIFELONG NON-SMOKER                                   26        1       18
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V19, continuous
D2V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       29             1        0        3
  subtype2           3       20             0        1        8
  subtype3           5       17             3        0        4
  subtype4           6       22             5        0        6
  subtype5           0        4             2        0        1
  subtype6           3       12             4        0        3
D2V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMBINATION          3        3        5        6        0        3
  EXTERNAL            29       20       17       22        4       12
  EXTERNAL BEAM        1        0        3        5        2        4
  IMPLANTS             0        1        0        0        0        0
  INTERNAL             3        8        4        6        1        3
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V22, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 2 0
  subtype3 7 1
  subtype4 8 2
  subtype5 2 0
  subtype6 6 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    2    0
  subtype3    7    1
  subtype4    8    2
  subtype5    2    0
  subtype6    6    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMPLETED AS PLANNED           4        2        7        8        2        6
  TREATMENT NOT COMPLETED        0        0        1        2        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   6
  subtype2                  0                0                   6
  subtype3                  0                1                   6
  subtype4                  1                1                  12
  subtype5                  0                0                   3
  subtype6                  0                0                   5
          vv
clus       REGIONAL SITE
  subtype1             4
  subtype2            12
  subtype3             6
  subtype4             6
  subtype5             2
  subtype6             3
D2V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  DISTANT RECURRENCE         1        0        0        1        0        0
  LOCAL RECURRENCE           0        0        1        1        0        0
  PRIMARY TUMOR FIELD        6        6        6       12        3        5
  REGIONAL SITE              4       12        6        6        2        3
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
          cls
clus        0  1
  subtype1 11  0
  subtype2 14  1
  subtype3 11  1
  subtype4 13  3
  subtype5  3  0
  subtype6  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    0
  subtype2   14    1
  subtype3   11    1
  subtype4   13    3
  subtype5    3    0
  subtype6    6    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CGY       11       14       11       13        3        6
  GY         0        1        1        3        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V25, continuous
D2V26, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      26       23       20       22        2       18 
  [1] "subtype2" "subtype3" "subtype4" "subtype6" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
 [13] "subtype1" "subtype3" "subtype6" "subtype1" "subtype1" "subtype6"
 [19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype6" "subtype4"
 [25] "subtype3" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [31] "subtype4" "subtype2" "subtype1" "subtype1" "subtype4" "subtype1"
 [37] "subtype1" "subtype6" "subtype3" "subtype4" "subtype3" "subtype6"
 [43] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype6"
 [49] "subtype3" "subtype6" "subtype6" "subtype2" "subtype4" "subtype3"
 [55] "subtype2" "subtype4" "subtype3" "subtype6" "subtype1" "subtype1"
 [61] "subtype4" "subtype3" "subtype2" "subtype2" "subtype6" "subtype6"
 [67] "subtype3" "subtype2" "subtype3" "subtype4" "subtype1" "subtype1"
 [73] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype1"
 [79] "subtype2" "subtype1" "subtype2" "subtype1" "subtype6" "subtype6"
 [85] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype2"
 [91] "subtype3" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [97] "subtype2" "subtype1" "subtype6" "subtype4" "subtype2" "subtype1"
[103] "subtype6" "subtype6" "subtype4" "subtype6" "subtype2" "subtype1"
[109] "subtype3"
D2V27, continuous
D2V28, continuous
D2V29, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      28       24       22       24        2       21 
  [1] "subtype2" "subtype4" "subtype4" "subtype6" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
 [13] "subtype1" "subtype3" "subtype6" "subtype1" "subtype1" "subtype6"
 [19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype6" "subtype4"
 [25] "subtype3" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [31] "subtype4" "subtype2" "subtype1" "subtype1" "subtype4" "subtype1"
 [37] "subtype1" "subtype6" "subtype3" "subtype4" "subtype3" "subtype6"
 [43] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype6"
 [49] "subtype3" "subtype6" "subtype6" "subtype2" "subtype4" "subtype3"
 [55] "subtype2" "subtype4" "subtype3" "subtype6" "subtype1" "subtype1"
 [61] "subtype4" "subtype3" "subtype2" "subtype2" "subtype6" "subtype6"
 [67] "subtype6" "subtype3" "subtype2" "subtype3" "subtype4" "subtype1"
 [73] "subtype1" "subtype2" "subtype1" "subtype1" "subtype4" "subtype2"
 [79] "subtype6" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype1" "subtype2" "subtype1" "subtype6" "subtype3"
 [91] "subtype6" "subtype2" "subtype2" "subtype1" "subtype4" "subtype1"
 [97] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
[103] "subtype2" "subtype2" "subtype1" "subtype6" "subtype4" "subtype2"
[109] "subtype1" "subtype6" "subtype6" "subtype3" "subtype4" "subtype6"
[115] "subtype4" "subtype6" "subtype2" "subtype1" "subtype3"
D2V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       8
  subtype2                                   2                       5
  subtype3                                   0                      11
  subtype4                                   2                       7
  subtype5                                   1                       2
  subtype6                                   2                       6
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       0                       2
  subtype3                       0                       2
  subtype4                       1                       1
  subtype5                       0                       0
  subtype6                       0                       3
D2V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        0        2
  OTHER LOCATION, SPECIFY                    8        5       11        7
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    2        2        2        1
                                     clus
vv                                    subtype5 subtype6
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2
  OTHER LOCATION, SPECIFY                    2        6
  POSITIVE BLADDER MARGIN                    0        0
  POSITIVE VAGINAL MARGIN                    0        3
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
  subtype6                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              9
  subtype2                                              6
  subtype3                                              4
  subtype4                                              3
  subtype5                                              1
  subtype6                                              2
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                17
  subtype2                                                                                20
  subtype3                                                                                17
  subtype4                                                                                 8
  subtype5                                                                                 3
  subtype6                                                                                18
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           34
  subtype2                                                                                           17
  subtype3                                                                                           27
  subtype4                                                                                           27
  subtype5                                                                                            4
  subtype6                                                                                           15
D2V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       34
                                                                                              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)                  20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       17
                                                                                              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)                  17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              clus
vv                                                                                             subtype4
  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)                   8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              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)                   3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        4
                                                                                              clus
vv                                                                                             subtype6
  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)                  18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       15
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V33, binary
          cls
clus        0  1
  subtype1 22 20
  subtype2  7 17
  subtype3 16 14
  subtype4 12  9
  subtype5  2  4
  subtype6 12 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   20
  subtype2    7   17
  subtype3   16   14
  subtype4   12    9
  subtype5    2    4
  subtype6   12   15
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        22        7       16       12        2       12
  PRESENT       20       17       14        9        4       15
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V34, continuous
D2V35, continuous
D2V36, binary
          cls
clus        0  1
  subtype1  0 16
  subtype2  6 31
  subtype3 13 26
  subtype4 18 22
  subtype5  5  3
  subtype6 12 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   16
  subtype2    6   31
  subtype3   13   26
  subtype4   18   22
  subtype5    5    3
  subtype6   12   21
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0        6       13       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       16       31       26       22
                                          clus
vv                                         subtype5 subtype6
  KERATINIZING SQUAMOUS CELL CARCINOMA            5       12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        3       21
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          18         20
  subtype2            2          11         18
  subtype3            3           7         17
  subtype4            2          10         17
  subtype5            0           2          1
  subtype6            1           5         16
D2V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CURRENT USER        7        2        3        2        0        1
  FORMER USER        18       11        7       10        2        5
  NEVER USED         20       18       17       17        1       16
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V39, continuous
D2V40, binary
          cls
clus        0  1
  subtype1 31  5
  subtype2 15  2
  subtype3 18  5
  subtype4 15  1
  subtype5  2  2
  subtype6 18  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    5
  subtype2   15    2
  subtype3   18    5
  subtype4   15    1
  subtype5    2    2
  subtype6   18    3
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        31       15       18       15        2       18
  PRESENT        5        2        5        1        2        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         2     0
  subtype2           1         1     0
  subtype3           1         5     1
  subtype4           0         8     0
  subtype5           1         1     0
  subtype6           0         1     0
D2V41, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype5"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        7        8        2        1 
 [1] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
[13] "subtype4" "subtype3" "subtype3"
             clus
vv            subtype3 subtype4
  CARBOPLATIN        1        0
  CISPLATIN          5        8
  OTHER              1        0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V42, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 subtype6 
       1        1        5        4        6 
 [1] "subtype4" "subtype3" "subtype6" "subtype4" "subtype3" "subtype6"
 [7] "subtype4" "subtype6" "subtype6" "subtype3" "subtype6" "subtype3"
[13] "subtype6" "subtype4" "subtype3"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    0   6   25    7  1   4    2    3   9  0   0   4  1   0  2
  subtype2    0   6   13    7  2   1    0    2   5  1   1   4  4   0  4
  subtype3    0   7   15    3  2   1    3    1  11  0   0   3  3   0  3
  subtype4    0  11    7    5  0   1    1    2   9  1   1   3  1   1  5
  subtype5    0   1    2    1  0   0    1    0   0  0   0   2  0   0  1
  subtype6    1   5   10    8  1   3    0    2   3  0   0   1  1   0  2
D2V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1A1        0        0        0        0        0        1
  T1B         6        6        7       11        1        5
  T1B1       25       13       15        7        2       10
  T1B2        7        7        3        5        1        8
  T2          1        2        2        0        0        1
  T2A         4        1        1        1        0        3
  T2A1        2        0        3        1        1        0
  T2A2        3        2        1        2        0        2
  T2B         9        5       11        9        0        3
  T3          0        1        0        1        0        0
  T3A         0        1        0        1        0        0
  T3B         4        4        3        3        2        1
  T4          1        4        3        1        0        1
  TIS         0        0        0        1        0        0
  TX          2        4        3        5        1        2
[1] 15  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        26        10
  subtype2       0        0         0         0        6        13         6
  subtype3       0        1         0         0        7        18         4
  subtype4       2        0         0         0       13         9         6
  subtype5       1        0         0         1        1         2         1
  subtype6       1        0         1         0        5        10        11
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         3          1          2         9         0
  subtype2        1         0          0          1         6         1
  subtype3        1         1          2          0        10         0
  subtype4        0         4          1          1        12         0
  subtype5        0         0          1          0         2         0
  subtype6        2         1          0          3         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          7         0         5
  subtype2          1         10         4         4
  subtype3          0         11         3         1
  subtype4          2          8         1         1
  subtype5          0          2         0         0
  subtype6          0          4         1         1
D2V45, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        0        0        2        1        1
  STAGE IA          0        0        1        0        0        0
  STAGE IA1         0        0        0        0        0        1
  STAGE IA2         0        0        0        0        1        0
  STAGE IB          5        6        7       13        1        5
  STAGE IB1        26       13       18        9        2       10
  STAGE IB2        10        6        4        6        1       11
  STAGE II          1        1        1        0        0        2
  STAGE IIA         3        0        1        4        0        1
  STAGE IIA1        1        0        2        1        1        0
  STAGE IIA2        2        1        0        1        0        3
  STAGE IIB         9        6       10       12        2        4
  STAGE III         0        1        0        0        0        0
  STAGE IIIA        0        1        0        2        0        0
  STAGE IIIB        7       10       11        8        2        4
  STAGE IVA         0        4        3        1        0        1
  STAGE IVB         5        4        1        1        0        1
[1] 17  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 36 14
  subtype2 35  5
  subtype3 60 11
subtype1 subtype2 subtype3 
      50       40       71 
subtype1 subtype2 subtype3 
      14        5       11 
$subtype1
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH 
       12.39        11.44       144.16        31.40        46.32        38.99 
TCGA-C5-A1MN TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7X3 TCGA-DG-A2KH 
       40.93        18.02        17.85        20.42         9.34         1.12 
TCGA-DS-A0VK TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A3QE 
       36.76        17.52         8.28        39.55        31.36        25.02 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A97N 
       24.56        26.01         7.46        26.79        15.02         0.36 
TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
       26.27         1.45         0.03         0.36         1.18        47.77 
TCGA-EK-A3GN TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A40J 
        0.03        14.70        19.79         8.32        15.55         1.35 
TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LF TCGA-IR-A3LH TCGA-LP-A4AW 
        9.01        10.82        21.67        96.95        78.71         0.89 
TCGA-MU-A5YI TCGA-Q1-A5R3 TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-VS-A8QF 
       34.62        15.95        14.07        19.59         3.88        57.93 
TCGA-VS-A94X TCGA-ZJ-A8QR 
       16.64        19.13 

$subtype2
TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1MJ TCGA-C5-A2LY TCGA-C5-A7CK TCGA-C5-A8XJ 
      173.29        30.21         0.46        78.35       134.33       146.86 
TCGA-DG-A2KM TCGA-DS-A0VL TCGA-DS-A1OA TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ 
       40.04         2.66        28.90       127.36        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HU TCGA-EA-A44S TCGA-EA-A5ZF TCGA-EA-A6QX 
       30.90        31.53        33.30        12.66        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EX-A1H5 TCGA-FU-A57G TCGA-HG-A2PA 
       13.48        45.96         0.43        20.35         1.32        25.41 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LL TCGA-JW-A5VL TCGA-LP-A4AX TCGA-MA-AA3Z 
       14.93       147.39        36.36        15.58        12.49        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MY-A913 TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-VS-A8EK 
        8.52        11.38         5.49        17.56         9.34        27.25 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9V0 TCGA-ZJ-AAXA 
       21.30        19.69        18.84         1.41 

$subtype3
TCGA-C5-A1M5 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MP 
       67.46        35.01        57.73        53.16        35.61         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 
       33.90        73.18        73.45        83.05       100.14        33.24 
TCGA-C5-A7CG TCGA-C5-A8XI TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DS-A0VM 
      210.67         8.35        11.87        50.76        44.94       117.99 
TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-DS-A5RQ 
      118.65         8.75        28.31        12.36        22.98        16.83 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       13.05        14.50        26.40        14.50        12.82        14.89 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PM TCGA-EK-A2R7 
       13.91        14.99         6.64       113.16         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK 
        0.13        16.08         4.04         2.24         0.07         0.10 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-IR-A3LA 
        1.22        23.84         0.92         1.58         1.48       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JX-A3PZ TCGA-JX-A3Q0 
       66.81       117.40        81.96        29.85        21.11       195.85 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y 
        7.99         0.30         0.82        13.35        22.52        17.82 
TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A73P TCGA-Q1-A73R 
        9.17        13.87         5.42        20.84        15.88        15.39 
TCGA-Q1-A73S TCGA-UC-A7PF TCGA-VS-A9U5 TCGA-VS-A9UQ TCGA-WL-A834 
       19.36        93.99        44.94        35.97        26.01 

subtype1 subtype2 subtype3 
    0.03     0.43     0.07 
subtype1 subtype2 subtype3 
  144.16   173.29   210.67 
subtype1 subtype2 subtype3 
  17.685   19.625   17.820 
[1] "0.0 - 144.2 (17.7)" "0.4 - 173.3 (19.6)" "0.1 - 210.7 (17.8)"
D3V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 30  8  0  1
  subtype2 24  8  4  1
  subtype3 45 15  3  1
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       30       24       45
  T2        8        8       15
  T3        0        4        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 27  9
  subtype2 23  8
  subtype3 42 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    9
  subtype2   23    8
  subtype3   42   21
   clus
vv  subtype1 subtype2 subtype3
  0       27       23       42
  1        9        8       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"
D3V5, binary
          cls
clus        0  1
  subtype1 22  1
  subtype2 24  1
  subtype3 37  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    1
  subtype2   24    1
  subtype3   37    2
   clus
vv  subtype1 subtype2 subtype3
  0       22       24       37
  1        1        1        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               44
  subtype2             0                               42
  subtype3             1                               58
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             0
  subtype3                                             2
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   4
  subtype2                                   3
  subtype3                                  10
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         2
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            1
  subtype2                                            1
  subtype3                                            1
D3V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        1
  CERVICAL SQUAMOUS CELL CARCINOMA                    44       42       58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        0        2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  4        3       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        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"
D3V7, binary
          cls
clus        0  1
  subtype1  8 44
  subtype2  7 39
  subtype3 10 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   44
  subtype2    7   39
  subtype3   10   64
     clus
vv    subtype1 subtype2 subtype3
  NO         8        7       10
  YES       44       39       64
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         6
  subtype2                                1     6                         2
  subtype3                                1     5                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    37
  subtype2                                         0    32
  subtype3                                         0    55
D3V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        1
  ASIAN                                            4        6        5
  BLACK OR AFRICAN AMERICAN                        6        2        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                           37       32       55
[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  1 40
  subtype2  6 26
  subtype3  6 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   40
  subtype2    6   26
  subtype3    6   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        6        6
  NOT HISPANIC OR LATINO       40       26       46
[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 21 10
  subtype2 26  5
  subtype3 40  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   10
  subtype2   26    5
  subtype3   40    9
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       21       26       40
  WITH TUMOR       10        5        9
[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       BRAZIL CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      2      1      5       3            38       3
  subtype2      4      1      5       1            30       5
  subtype3      2      2      2       3            60       5
D3V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL               2        4        2
  CANADA               1        1        2
  RUSSIA               5        5        2
  UKRAINE              3        1        3
  UNITED STATES       38       30       60
  VIETNAM              3        5        5
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  3 24 19  1  4
  subtype2  2 24 14  0  3
  subtype3  5 27 40  0  1
D3V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        3        2        5
  G2       24       24       27
  G3       19       14       40
  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"
D3V16, continuous
D3V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  subtype2                                           7
  subtype3                                          13
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      2
  subtype3                                      2
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              6
  subtype2                                               2              3
  subtype3                                               0             14
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  27
  subtype2                  26
  subtype3                  33
D3V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        7       13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        0
  CURRENT SMOKER                                         6        3       14
  LIFELONG NON-SMOKER                                   27       26       33
[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"
D3V19, continuous
D3V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           5       15             4        0        3
  subtype2           2       12             3        1        3
  subtype3           5       23             6        0        2
D3V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          5        2        5
  EXTERNAL            15       12       23
  EXTERNAL BEAM        4        3        6
  IMPLANTS             0        1        0
  INTERNAL             3        3        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"
D3V22, binary
          cls
clus       0 1
  subtype1 7 1
  subtype2 5 1
  subtype3 9 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    5    1
  subtype3    9    0
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           7        5        9
  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"
          vv
clus       LOCAL RECURRENCE PRIMARY TUMOR FIELD REGIONAL SITE
  subtype1                2                   5             3
  subtype2                0                   6             1
  subtype3                0                   9             1
D3V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  LOCAL RECURRENCE           2        0        0
  PRIMARY TUMOR FIELD        5        6        9
  REGIONAL SITE              3        1        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"
D3V24, binary
          cls
clus       0 1
  subtype1 6 3
  subtype2 4 1
  subtype3 8 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2    4    1
  subtype3    8    0
     clus
vv    subtype1 subtype2 subtype3
  CGY        6        4        8
  GY         3        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"
D3V25, continuous
D3V26, continuous
D3V27, continuous
D3V28, continuous
D3V29, continuous
D3V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       3
  subtype2                                   1                       6
  subtype3                                   5                      15
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       2
  subtype2                       0                       0
  subtype3                       0                       3
D3V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        5
  OTHER LOCATION, SPECIFY                    3        6       15
  POSITIVE BLADDER MARGIN                    1        0        0
  POSITIVE VAGINAL MARGIN                    2        0        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                                             1
  subtype3                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              2
  subtype2                                              5
  subtype3                                              6
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                12
  subtype2                                                                                12
  subtype3                                                                                22
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           29
  subtype2                                                                                           18
  subtype3                                                                                           31
D3V32, 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)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       29
                                                                                              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)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       18
                                                                                              clus
vv                                                                                             subtype3
  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)                  22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       31
[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"
D3V33, binary
          cls
clus        0  1
  subtype1 20 13
  subtype2 14 12
  subtype3 18 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   13
  subtype2   14   12
  subtype3   18   34
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        20       14       18
  PRESENT       13       12       34
[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"
D3V34, continuous
D3V35, continuous
D3V36, binary
          cls
clus        0  1
  subtype1 12 27
  subtype2  6 25
  subtype3 21 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   27
  subtype2    6   25
  subtype3   21   23
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           12        6       21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       27       25       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"
D3V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           9         14
  subtype2            0           7         17
  subtype3            5          15         20
D3V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        0        0        5
  FORMER USER         9        7       15
  NEVER USED         14       17       20
[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"
D3V39, continuous
D3V40, binary
          cls
clus        0  1
  subtype1 23  2
  subtype2 24  1
  subtype3 37  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    2
  subtype2   24    1
  subtype3   37    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       24       37
  PRESENT        2        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         3     1
  subtype2           1         3     0
  subtype3           1         7     0
D3V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        1
  CISPLATIN          3        3        7
  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"
D3V42, continuous
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    1   7   14    8  0   0    3    2   3  0   0   0  1   0  5
  subtype2    0   6   13    5  0   2    0    2   4  0   1   3  1   1  2
  subtype3    0  10   25   10  3   2    3    3   4  1   0   2  1   0  1
D3V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A1        1        0        0
  T1B         7        6       10
  T1B1       14       13       25
  T1B2        8        5       10
  T2          0        0        3
  T2A         0        2        2
  T2A1        3        0        3
  T2A2        2        2        3
  T2B         3        4        4
  T3          0        0        1
  T3A         0        1        0
  T3B         0        3        2
  T4          1        1        1
  TIS         0        1        0
  TX          5        2        1
[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"
D3V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        6        13        12
  subtype2       2        0         0         1        8        11         4
  subtype3       1        0         0         0       13        24        11
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         1          1          1         7         0
  subtype2        3         2          0          0         5         0
  subtype3        1         2          3          3         4         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          5         1         1
  subtype2          1          7         2         0
  subtype3          0          7         1         1
D3V45, 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          6        8       13
  STAGE IB1        13       11       24
  STAGE IB2        12        4       11
  STAGE II          0        3        1
  STAGE IIA         1        2        2
  STAGE IIA1        1        0        3
  STAGE IIA2        1        0        3
  STAGE IIB         7        5        4
  STAGE III         0        0        1
  STAGE IIIA        0        1        0
  STAGE IIIB        5        7        7
  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 24  6
  subtype2 40  7
  subtype3 39  8
  subtype4 15  6
  subtype5 13  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       47       47       21       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        7        8        6        3 
$subtype1
TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A3HE TCGA-C5-A3HF 
       11.44       144.16        46.32        38.99        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7X3 TCGA-EA-A1QS TCGA-EA-A3QE TCGA-EA-A5FO TCGA-EA-A5ZD 
       20.42         9.34        39.55        25.02        26.79        15.02 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EK-A2RE TCGA-EX-A449 TCGA-EX-A69L 
        0.36        26.27         1.45         0.36        14.70        19.79 
TCGA-FU-A40J TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LF TCGA-LP-A4AW 
        1.35         9.01        10.82        21.67        96.95         0.89 
TCGA-MU-A5YI TCGA-Q1-A5R3 TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-ZJ-A8QR 
       34.62        15.95        14.07        19.59         3.88        19.13 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MP TCGA-C5-A2LT 
       12.39        35.01        57.73        53.16         3.58        73.18 
TCGA-C5-A2LX TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DS-A0VN 
       83.05        33.24       210.67         1.12        44.94       118.65 
TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       28.31        22.98        16.83        13.05        14.50        26.40 
TCGA-EA-A556 TCGA-EK-A2IR TCGA-EK-A2PM TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL 
       14.89       113.16         0.59         4.04         0.03        47.77 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3TX 
        2.24         0.07         8.32        15.55         0.92         1.48 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JX-A5QV 
      137.16        66.81       117.40        81.96        29.85         7.99 
TCGA-LP-A5U2 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF 
        0.30        22.52        17.82        13.87         5.42        20.84 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-VS-A9UQ TCGA-WL-A834 
       15.88        15.39        19.36        35.97        26.01 

$subtype3
TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1MI TCGA-C5-A1MQ TCGA-C5-A2LZ 
      173.29        67.46        30.21        35.61        33.90       100.14 
TCGA-C5-A7CK TCGA-C5-A8XJ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VM 
      134.33       146.86        11.87        50.76        40.04       117.99 
TCGA-DS-A1O9 TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
        8.75        12.36       127.36        12.36        37.35        31.53 
TCGA-EA-A3HU TCGA-EA-A44S TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       33.30        12.66        13.91        14.99        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A3TQ 
       45.96         0.43         0.10        20.35         1.22         1.58 
TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U3 TCGA-MA-AA3Z 
       14.93        36.36        15.58       195.85         0.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-Q1-A6DW TCGA-UC-A7PF TCGA-VS-A8EK 
        9.17         8.52        11.38        17.56        93.99        27.25 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9V0 
       57.93        16.64        44.94        19.69        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 
        2.66         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         1.18         0.03        78.71        21.11        12.49 
TCGA-MY-A913 TCGA-Q1-A73Q TCGA-VS-A9UB 
        5.49         9.34        21.30 

$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        14.50        12.82 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-FU-A23L TCGA-FU-A57G 
       14.96         0.59         0.13        16.08        23.84         1.32 
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     0.03     0.10     0.03     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
  144.16   210.67   195.85    78.71   147.39 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.935   19.360   19.690   21.110   14.730 
[1] "0.4 - 144.2 (17.9)" "0.0 - 210.7 (19.4)" "0.1 - 195.8 (19.7)"
[4] "0.0 - 78.7 (21.1)"  "0.1 - 147.4 (14.7)"
D4V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 19  3  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        3        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 16  4
  subtype2 30 12
  subtype3 19 14
  subtype4 13  6
  subtype5 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    4
  subtype2   30   12
  subtype3   19   14
  subtype4   13    6
  subtype5   14    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       16       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 11  1
  subtype2 24  1
  subtype3 26  1
  subtype4 12  1
  subtype5 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   24    1
  subtype3   26    1
  subtype4   12    1
  subtype5   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       11       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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             1                               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                                   6
          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                                            0
D4V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        1        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        6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  6 25
  subtype2  7 42
  subtype3  8 43
  subtype4  3 20
  subtype5  1 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   25
  subtype2    7   42
  subtype3    8   43
  subtype4    3   20
  subtype5    1   17
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         6        7        8        3        1
  YES       25       42       43       20       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"
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    22
  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                                           22       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 27
  subtype2  3 29
  subtype3  6 29
  subtype4  1 14
  subtype5  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   27
  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       27       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 12  5
  subtype2 28  5
  subtype3 30  6
  subtype4  9  4
  subtype5  8  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    5
  subtype2   28    5
  subtype3   30    6
  subtype4    9    4
  subtype5    8    4
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       12       28       30        9        8
  WITH TUMOR        5        5        6        4        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       BRAZIL CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      0      0      2       2            24       3
  subtype2      1      2      3       1            41       1
  subtype3      6      2      4       2            33       4
  subtype4      1      0      2       1            17       2
  subtype5      0      0      1       1            13       3
D4V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  BRAZIL               0        1        6        1        0
  CANADA               0        2        2        0        0
  RUSSIA               2        3        4        2        1
  UKRAINE              2        1        2        1        1
  UNITED STATES       24       41       33       17       13
  VIETNAM              3        1        4        2        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"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  2 15 11  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
D4V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        2        5        2        1        0
  G2       15       16       26        9        9
  G3       11       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"
D4V16, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       11       10        1        3 
 [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype5" "subtype2" "subtype2"
[13] "subtype2" "subtype3" "subtype5" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3"
D4V17, 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"
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           2
  subtype2                                          10
  subtype3                                          11
  subtype4                                           2
  subtype5                                           2
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      2
  subtype3                                      1
  subtype4                                      0
  subtype5                                      1
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              4
  subtype2                                               0              6
  subtype3                                               1              7
  subtype4                                               1              5
  subtype5                                               0              1
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  18
  subtype2                  21
  subtype3                  24
  subtype4                  11
  subtype5                  12
D4V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            2       10       11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        2        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        0        1
  CURRENT SMOKER                                         4        6        7
  LIFELONG NON-SMOKER                                   18       21       24
                                                 clus
vv                                                subtype4 subtype5
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            2        2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0
  CURRENT SMOKER                                         5        1
  LIFELONG NON-SMOKER                                   11       12
[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"
D4V19, continuous
D4V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3        9             3        0        1
  subtype2           2       14             5        0        3
  subtype3           4       16             4        0        2
  subtype4           3        6             1        0        2
  subtype5           0        5             0        1        0
D4V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  COMBINATION          3        2        4        3        0
  EXTERNAL             9       14       16        6        5
  EXTERNAL BEAM        3        5        4        1        0
  IMPLANTS             0        0        0        0        1
  INTERNAL             1        3        2        2        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"
D4V22, 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"
          vv
clus       LOCAL RECURRENCE PRIMARY TUMOR FIELD REGIONAL SITE
  subtype1                2                   3             1
  subtype2                0                   4             1
  subtype3                0                   9             2
  subtype4                0                   3             1
  subtype5                0                   1             0
D4V23, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        5       11        4        1 
 [1] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype1" "subtype3"
[13] "subtype1" "subtype4" "subtype3" "subtype2" "subtype4" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
[25] "subtype3" "subtype2"
                     clus
vv                    subtype1 subtype2 subtype3 subtype4
  LOCAL RECURRENCE           2        0        0        0
  PRIMARY TUMOR FIELD        3        4        9        3
  REGIONAL SITE              1        1        2        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"
D4V24, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 4 0
  subtype3 8 0
  subtype4 2 2
  subtype5 1 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    4    0
  subtype3    8    0
  subtype4    2    2
  subtype5    1    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  CGY        3        4        8        2        1
  GY         2        0        0        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"
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       3
  subtype2                                   4                      10
  subtype3                                   2                       6
  subtype4                                   0                       3
  subtype5                                   0                       2
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       0
  subtype2                       0                       2
  subtype3                       0                       1
  subtype4                       1                       2
  subtype5                       0                       0
D4V31, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       17        9        6        2 
 [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype4" "subtype2"
[13] "subtype1" "subtype1" "subtype2" "subtype4" "subtype2" "subtype4"
[19] "subtype4" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype1"
[31] "subtype3" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        4        2        0
  OTHER LOCATION, SPECIFY                    3       10        6        3
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    0        2        1        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                                             0
  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                                                                                           18
  subtype2                                                                                           23
  subtype3                                                                                           18
  subtype4                                                                                           12
  subtype5                                                                                            7
D4V32, 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)       18
                                                                                              clus
vv                                                                                             subtype2
  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)                  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"
D4V33, binary
          cls
clus        0  1
  subtype1 13  7
  subtype2 13 22
  subtype3 12 17
  subtype4  6  6
  subtype5  8  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    7
  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        7       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"
D4V34, continuous
D4V35, continuous
D4V36, binary
          cls
clus        0  1
  subtype1  7 17
  subtype2 16 14
  subtype3 10 25
  subtype4  6 11
  subtype5  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   17
  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       17       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"
D4V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           3          8
  subtype2            3          12         13
  subtype3            1           6         18
  subtype4            0           6          8
  subtype5            1           4          4
D4V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        0        3        1        0        1
  FORMER USER         3       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"
D4V39, continuous
D4V40, binary
          cls
clus        0  1
  subtype1 16  0
  subtype2 24  3
  subtype3 25  3
  subtype4  9  1
  subtype5 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    0
  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        0        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         2     1
  subtype2           1         4     0
  subtype3           0         5     0
  subtype4           0         2     0
  subtype5           1         0     0
D4V41, multiclass
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        5        5        2        1 
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[13] "subtype1"
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        0
  CISPLATIN          2        4        5
  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"
D4V42, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        5        2        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    1   7    7    4  0   0    1    1   1  0   0   0  0   0  3
  subtype2    0   7   16    8  1   2    2    2   2  0   0   2  0   0  1
  subtype3    0   5   15    4  1   1    0    2   7  1   1   2  2   0  2
  subtype4    0   3    7    3  0   0    1    1   1  0   0   1  1   1  2
  subtype5    0   1    7    4  1   1    2    1   0  0   0   0  0   0  0
D4V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5
  T1A1        1        0        0        0        0
  T1B         7        7        5        3        1
  T1B1        7       16       15        7        7
  T1B2        4        8        4        3        4
  T2          0        1        1        0        1
  T2A         0        2        1        0        1
  T2A1        1        2        0        1        2
  T2A2        1        2        2        1        1
  T2B         1        2        7        1        0
  T3          0        0        1        0        0
  T3A         0        0        1        0        0
  T3B         0        2        2        1        0
  T4          0        0        2        1        0
  TIS         0        0        0        1        0
  TX          3        1        2        2        0
[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"
D4V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        4         7         8
  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
D4V45, 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         8        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 42 11
  subtype2 77 22
  subtype3 52 15
  subtype4 47 21
subtype1 subtype2 subtype3 subtype4 
      53       99       67       68 
subtype1 subtype2 subtype3 subtype4 
      11       22       15       21 
$subtype1
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LX TCGA-C5-A7CK TCGA-C5-A8XJ 
       57.04        35.61        20.91        83.05       134.33       146.86 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DS-A0VK TCGA-DS-A1O9 TCGA-DS-A1OB 
       23.51        20.81        20.91        36.76         8.75        28.31 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A410 TCGA-EA-A439 
      127.36        22.98        39.55        13.05        26.40        14.50 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IR 
       12.82        14.89        14.99        14.96        12.59       113.16 
TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A3HZ 
       19.27         0.59         0.13         0.07        20.35        36.26 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A57G TCGA-HM-A3JK TCGA-HM-A6W2 
        1.45         1.48         0.82         1.32        20.78         9.44 
TCGA-JW-A5VH TCGA-JW-A5VK TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A5YI 
        3.29        20.48         0.89         0.30        13.35        34.62 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-VS-A8EC TCGA-VS-A8EJ 
       35.05         2.96         9.34        19.36        40.50        19.96 
TCGA-VS-A954 TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UP 
       50.63        43.40        19.69        14.53        43.27 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       12.39        49.48        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A3HL TCGA-C5-A7CG 
       38.99         2.43         3.58       100.14        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A8XI TCGA-C5-A901 
      101.82        15.48       147.35       155.77         8.35        17.03 
TCGA-C5-A905 TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
      160.41        44.94        40.04        87.75        58.88         2.66 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       28.90        16.83        12.36        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        12.66         7.46        13.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2RA 
       15.02        13.58        13.48         0.36         1.51        16.08 
TCGA-EK-A2RB TCGA-EK-A2RN TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ 
        0.07         0.10        23.84         0.92        31.36         1.58 
TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VJ 
        3.52         1.97        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       195.85         7.99         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        13.87         5.42        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        37.78        26.43 
TCGA-VS-A8EK TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       27.25        32.15        11.51        57.93        31.27        36.26 
TCGA-VS-A94Z TCGA-VS-A9U7 TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV 
       24.39        42.41        40.96        27.25        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAX4 
       18.25        14.04        14.89        26.01        29.26         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

$subtype3
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       23.67        31.40        35.01        57.73        53.16         0.46 
TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM 
       44.22        38.43        33.24        18.02        17.85        20.35 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF 
        2.73        50.99         1.12        58.88        50.76        16.18 
TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A5FO TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RL 
       17.52        24.56        26.79         0.59         4.04        47.77 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF 
        2.24         0.10         7.92        14.70         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A770 TCGA-HG-A2PA TCGA-IR-A3L7 
        1.22         2.17         1.35         1.12        25.41       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A69B 
      137.16        66.81       117.40        96.95        81.96        28.37 
TCGA-JX-A3Q8 TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73P 
       30.31        54.81        15.58        15.95        16.14        15.88 
TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       15.39         3.88        66.05        36.13        39.78        50.86 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO 
       48.07        45.34        44.94        22.72         1.71        41.42 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 
       35.97        20.09        67.20        18.84         5.16         4.34 
TCGA-VS-A9V5 
       16.24 

$subtype4
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A1MQ TCGA-C5-A2LT 
       11.44        18.74         5.46        40.93        33.90        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UH 
       73.45        78.35        52.01       154.32        17.19       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR 
       94.95         9.34        13.61        45.83        99.91        27.52 
TCGA-C5-A902 TCGA-C5-A907 TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A7WI 
        4.90        11.87       117.99       118.65        12.36         8.28 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       14.50        26.01        45.96        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         0.36         1.18         0.10         0.03         6.94 
TCGA-EX-A69L TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI 
       19.79         9.01        78.71        29.85        27.42        24.56 
TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA41 
       15.58        21.11        11.28        12.49        17.82         9.17 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V TCGA-UC-A7PD 
       11.38         5.49         9.04        14.07        19.59        11.67 
TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y 
       10.03        18.05        59.51        46.03        16.64         4.73 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-AA62 
       39.78        15.68        50.14        21.30        46.92        15.42 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       67.59        19.13 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.10     0.03 
subtype1 subtype2 subtype3 subtype4 
  146.86   210.67   147.39   154.32 
subtype1 subtype2 subtype3 subtype4 
  19.960   20.840   23.670   17.935 
[1] "0.1 - 146.9 (20.0)" "0.1 - 210.7 (20.8)" "0.1 - 147.4 (23.7)"
[4] "0.0 - 154.3 (17.9)"
D5V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 22 13  6  3
  subtype2 48 26  7  4
  subtype3 40 14  2  1
  subtype4 29 16  5  2
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       22       48       40       29
  T2       13       26       14       16
  T3        6        7        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 22 11
  subtype2 45 27
  subtype3 35 10
  subtype4 29 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   11
  subtype2   45   27
  subtype3   35   10
  subtype4   29   11
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       22       45       35       29
  1       11       27       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 23  4
  subtype2 43  1
  subtype3 23  2
  subtype4 26  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    4
  subtype2   43    1
  subtype3   23    2
  subtype4   26    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       23       43       23       26
  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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               47
  subtype2             0                              104
  subtype3             2                               28
  subtype4             0                               72
          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                                  19
  subtype4                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         1
  subtype2                                         0
  subtype3                                         2
  subtype4                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            1
  subtype2                                            0
  subtype3                                           14
  subtype4                                            0
D5V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    47      104       28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        2        0        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  3        0       19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            1        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        0       14
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    72
  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"
D5V7, binary
          cls
clus        0  1
  subtype1  8 48
  subtype2 12 92
  subtype3  4 65
  subtype4 11 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   48
  subtype2   12   92
  subtype3    4   65
  subtype4   11   61
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8       12        4       11
  YES       48       92       65       61
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     6                         7
  subtype2                                1     7                        11
  subtype3                                0     2                         1
  subtype4                                4     4                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    35
  subtype2                                         0    71
  subtype3                                         0    55
  subtype4                                         2    47
D5V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 2        1        0        4
  ASIAN                                            6        7        2        4
  BLACK OR AFRICAN AMERICAN                        7       11        1       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           35       71       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 38
  subtype2  8 58
  subtype3  5 32
  subtype4  9 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   38
  subtype2    8   58
  subtype3    5   32
  subtype4    9   39
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        8        5        9
  NOT HISPANIC OR LATINO       38       58       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 22 13
  subtype2 52 13
  subtype3 34  9
  subtype4 29  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   13
  subtype2   52   13
  subtype3   34    9
  subtype4   29    9
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       22       52       34       29
  WITH TUMOR       13       13        9        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      7      0       1      3       1            38       6
  subtype2     18      2       0      8       3            68       5
  subtype3     16      3       0      1       1            48       0
  subtype4     12      0       0      0       2            55       3
D5V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  BRAZIL               7       18       16       12
  CANADA               0        2        3        0
  NIGERIA              1        0        0        0
  RUSSIA               3        8        1        0
  UKRAINE              1        3        1        2
  UNITED STATES       38       68       48       55
  VIETNAM              6        5        0        3
[1] 7 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 28  0  2
  subtype2  7 62 28  0  6
  subtype3  7 30 25  0  7
  subtype4  2 21 35  1  9
D5V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        2        7        7        2
  G2       22       62       30       21
  G3       28       28       25       35
  G4        0        0        0        1
  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"
D5V16, continuous
D5V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           6
  subtype2                                          14
  subtype3                                          11
  subtype4                                           8
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      3
  subtype2                                      5
  subtype3                                      1
  subtype4                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             14
  subtype2                                               2             25
  subtype3                                               0              9
  subtype4                                               1             16
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  21
  subtype2                  48
  subtype3                  39
  subtype4                  35
D5V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            6       14       11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 3        5        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        2        0
  CURRENT SMOKER                                        14       25        9
  LIFELONG NON-SMOKER                                   21       48       39
                                                 clus
vv                                                subtype4
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1
  CURRENT SMOKER                                        16
  LIFELONG NON-SMOKER                                   35
[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"
D5V19, continuous
D5V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       20             5        0        2
  subtype2           8       31             4        1       10
  subtype3           3       29             1        0        4
  subtype4           6       24             5        0        8
D5V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  COMBINATION          3        8        3        6
  EXTERNAL            20       31       29       24
  EXTERNAL BEAM        5        4        1        5
  IMPLANTS             0        1        0        0
  INTERNAL             2       10        4        8
[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"
D5V22, 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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  0                0                   7
  subtype2                  0                1                  12
  subtype3                  1                0                   5
  subtype4                  1                1                  14
          vv
clus       REGIONAL SITE
  subtype1             6
  subtype2            13
  subtype3             6
  subtype4             7
D5V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3 subtype4
  DISTANT RECURRENCE         0        0        1        1
  LOCAL RECURRENCE           0        1        0        1
  PRIMARY TUMOR FIELD        7       12        5       14
  REGIONAL SITE              6       13        6        7
[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"
D5V24, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 21  1
  subtype3 11  1
  subtype4 15  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   21    1
  subtype3   11    1
  subtype4   15    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  CGY       10       21       11       15
  GY         0        1        1        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"
D5V25, continuous
D5V26, continuous
D5V27, continuous
D5V28, continuous
D5V29, continuous
D5V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       3
  subtype2                                   2                      17
  subtype3                                   2                      10
  subtype4                                   3                       9
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       3
  subtype2                       1                       4
  subtype3                       0                       2
  subtype4                       0                       1
D5V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        2        3
  OTHER LOCATION, SPECIFY                    3       17       10        9
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    3        4        2        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                                             2
  subtype3                                             0
  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                                                                                20
  subtype2                                                                                35
  subtype3                                                                                19
  subtype4                                                                                 7
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           20
  subtype2                                                                                           38
  subtype3                                                                                           30
  subtype4                                                                                           35
D5V32, 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)                  20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       20
                                                                                              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)                  35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       38
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  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)       35
[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"
D5V33, binary
          cls
clus        0  1
  subtype1 12 18
  subtype2 26 29
  subtype3 18 21
  subtype4 14 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   18
  subtype2   26   29
  subtype3   18   21
  subtype4   14   10
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        12       26       18       14
  PRESENT       18       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"
D5V34, continuous
D5V35, continuous
D5V36, binary
          cls
clus        0  1
  subtype1 15 20
  subtype2 20 54
  subtype3  1 16
  subtype4 18 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   20
  subtype2   20   54
  subtype3    1   16
  subtype4   18   28
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA           15       20        1       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       20       54       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"
D5V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0          11         19
  subtype2            3          15         31
  subtype3            8          15         18
  subtype4            4          11         20
D5V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        0        3        8        4
  FORMER USER        11       15       15       11
  NEVER USED         19       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"
D5V39, continuous
D5V40, binary
          cls
clus        0  1
  subtype1 18  4
  subtype2 32 10
  subtype3 28  4
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    4
  subtype2   32   10
  subtype3   28    4
  subtype4   21    0
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        18       32       28       21
  PRESENT        4       10        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           1         4     0
  subtype2           2         5     0
  subtype3           0         1     0
  subtype4           0         8     1
D5V41, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        7        1        9 
 [1] "subtype2" "subtype2" "subtype4" "subtype2" "subtype1" "subtype2"
 [7] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype4"
[13] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
[19] "subtype4" "subtype4" "subtype2"
             clus
vv            subtype1 subtype2 subtype4
  CARBOPLATIN        1        2        0
  CISPLATIN          4        5        8
  OTHER              0        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"
D5V42, 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"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    1   2   13    6  2   3    1    3   4  0   1   5  3   0  1
  subtype2    0  16   21   11  2   4    2    4  14  1   0   6  4   0  7
  subtype3    0   7   26    7  0   2    2    1   9  0   0   2  1   0  3
  subtype4    0  11   11    7  2   1    2    2   9  0   1   4  2   1  6
D5V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4
  T1A1        1        0        0        0
  T1B         2       16        7       11
  T1B1       13       21       26       11
  T1B2        6       11        7        7
  T2          2        2        0        2
  T2A         3        4        2        1
  T2A1        1        2        2        2
  T2A2        3        4        1        2
  T2B         4       14        9        9
  T3          0        1        0        0
  T3A         1        0        0        1
  T3B         5        6        2        4
  T4          3        4        1        2
  TIS         0        0        0        1
  TX          1        7        3        6
[1] 15  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        4        13         7
  subtype2       1        0         0         1       15        22        10
  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          1          4         6         0
  subtype2        4         2          2          2        12         1
  subtype3        0         2          0          0        10         0
  subtype4        0         4          2          1        14         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          1          9         2         3
  subtype2          0         19         4         5
  subtype3          0          5         1         3
  subtype4          1          9         2         1
D5V45, 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          4       15        5       13
  STAGE IB1        13       22       31       11
  STAGE IB2         7       10       10       11
  STAGE II          1        4        0        0
  STAGE IIA         1        2        2        4
  STAGE IIA1        1        2        0        2
  STAGE IIA2        4        2        0        1
  STAGE IIB         6       12       10       14
  STAGE III         0        1        0        0
  STAGE IIIA        1        0        0        1
  STAGE IIIB        9       19        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  51  17
  subtype2 145  39
  subtype3  22  13
subtype1 subtype2 subtype3 
      68      184       35 
subtype1 subtype2 subtype3 
      17       39       13 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS 
       31.40        35.01        57.73        35.61         0.46        44.22 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT 
       38.43        33.24        18.02        20.35         2.73        20.81 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 
        1.12        58.88        50.76        16.18        17.52        26.40 
TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2R7 
       14.50        12.82        14.89        26.79        14.96         0.59 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF 
       47.77         2.24         0.10         7.92        14.70        15.55 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.22         2.17        36.26         1.35         1.32         1.12 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH 
        9.44       137.16        66.81        96.95        81.96         3.29 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 
       28.37        30.31        13.35        54.81         2.96        15.58 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EJ 
       16.14        15.88        15.39        19.36        66.05        19.96 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO 
       36.13        39.78        50.86         1.71        14.53        41.42 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       43.27        35.97        20.09        67.20        18.84         5.16 
TCGA-VS-A9V4 TCGA-VS-A9V5 
        4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI 
       12.39        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-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A905 
        8.35       146.86        23.51        20.91        17.03       160.41 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
      117.99       118.65         8.75        28.90        28.31        12.36 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
      127.36        22.98        16.83        39.55        12.36        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
       30.90        31.53        31.36        33.30        13.05        25.02 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.56        12.66         7.46        13.91        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       13.58        13.48         0.36        12.59        45.96         6.64 
TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 
      113.16         1.51        19.27         0.43         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A2RO 
       16.08         0.07         4.04         0.36         0.10         0.07 
TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG 
        0.10        20.35        19.79         8.32        23.84         0.92 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
        1.97        25.41        21.67        20.78        14.93       147.39 
TCGA-IR-A3LC TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
      117.40        29.85        36.36        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU 
       15.58         8.28        18.15       195.85         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89         0.30         0.82        22.52        20.28        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         9.17         8.52        11.38        13.87        34.62 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.42        35.05        20.84        16.41        15.95         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
       17.56        14.07         9.34        19.59         3.88        93.99 
TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK 
       12.16        40.50        37.78        26.43        18.05        27.25 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       59.51        32.15        11.51        57.93        31.27        36.26 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       24.39        39.78        15.68        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UD 
       45.34        44.94        43.40        42.41        22.72        19.69 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       46.92        40.96        27.25        14.53         3.42        18.25 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       14.04        14.89        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         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        11.87         8.28        14.50        26.01        26.27 
TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-GH-A9DA TCGA-IR-A3LH 
        1.45         1.18         0.03         6.94         9.01        78.71 
TCGA-JW-A5VG TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-UC-A7PD TCGA-VS-A8EB 
       27.42        21.11        12.49         5.49        11.67        10.03 
TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-AA62 
       46.03        16.64         4.73        21.30        15.42 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  137.16   210.67    99.91 
subtype1 subtype2 subtype3 
   18.43    20.91    15.42 
[1] "0.1 - 137.2 (18.4)" "0.1 - 210.7 (20.9)" "0.0 - 99.9 (15.4)" 
D6V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 38 19  3  2
  subtype2 86 41 16  8
  subtype3 15  9  1  0
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       38       86       15
  T2       19       41        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 37 12
  subtype2 77 42
  subtype3 17  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   12
  subtype2   77   42
  subtype3   17    5
   clus
vv  subtype1 subtype2 subtype3
  0       37       77       17
  1       12       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 26  5
  subtype2 77  3
  subtype3 12  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    5
  subtype2   77    3
  subtype3   12    2
   clus
vv  subtype1 subtype2 subtype3
  0       26       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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             4                               22
  subtype2             0                              192
  subtype3             0                               37
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  22
  subtype2                                   0
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           14
  subtype2                                            1
  subtype3                                            0
D6V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    22      192       37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 22        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        14        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"
D6V7, binary
          cls
clus         0   1
  subtype1   3  67
  subtype2  25 169
  subtype3   7  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   67
  subtype2   25  169
  subtype3    7   30
     clus
vv    subtype1 subtype2 subtype3
  NO         3       25        7
  YES       67      169       30
[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"
D6V8, continuous
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                4    13                        20
  subtype3                                2     1                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    52
  subtype2                                         2   130
  subtype3                                         0    26
D6V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        4        2
  ASIAN                                            5       13        1
  BLACK OR AFRICAN AMERICAN                        3       20        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        2        0
  WHITE                                           52      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  37
  subtype2  16 108
  subtype3   2  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   37
  subtype2   16  108
  subtype3    2   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       16        2
  NOT HISPANIC OR LATINO       37      108       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 32 12
  subtype2 93 28
  subtype3 12  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   12
  subtype2   93   28
  subtype3   12    4
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       32       93       12
  WITH TUMOR       12       28        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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     15      3       1      2       2            44       3
  subtype2     32      2       0     10       3           137      10
  subtype3      6      0       0      0       2            28       1
D6V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              15       32        6
  CANADA               3        2        0
  NIGERIA              1        0        0
  RUSSIA               2       10        0
  UKRAINE              2        3        2
  UNITED STATES       44      137       28
  VIETNAM              3       10        1
[1] 7 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 27  0  6
  subtype2 10 93 69  0 16
  subtype3  1 12 20  1  2
D6V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        7       10        1
  G2       30       93       12
  G3       27       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"
D6V16, continuous
D6V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           8
  subtype2                                          27
  subtype3                                           4
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      8
  subtype3                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             11
  subtype2                                               3             43
  subtype3                                               1             10
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  43
  subtype2                  85
  subtype3                  15
D6V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            8       27        4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        8        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        3        1
  CURRENT SMOKER                                        11       43       10
  LIFELONG NON-SMOKER                                   43       85       15
[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"
D6V19, continuous
D6V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           2       31             1        0        5
  subtype2          13       59            12        1       14
  subtype3           5       14             2        0        5
D6V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          2       13        5
  EXTERNAL            31       59       14
  EXTERNAL BEAM        1       12        2
  IMPLANTS             0        1        0
  INTERNAL             5       14        5
[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"
D6V22, 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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   6
  subtype2                  0                1                  22
  subtype3                  1                1                  10
          vv
clus       REGIONAL SITE
  subtype1             6
  subtype2            23
  subtype3             3
D6V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        6       22       10
  REGIONAL SITE              6       23        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"
D6V24, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 35  2
  subtype3 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   35    2
  subtype3   10    2
     clus
vv    subtype1 subtype2 subtype3
  CGY       12       35       10
  GY         1        2        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"
D6V25, continuous
D6V26, continuous
D6V27, continuous
D6V28, continuous
D6V29, continuous
D6V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       8
  subtype2                                   5                      26
  subtype3                                   2                       5
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       7
  subtype3                       0                       1
D6V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        5        2
  OTHER LOCATION, SPECIFY                    8       26        5
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        7        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                                             0
          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                                                                                18
  subtype2                                                                                61
  subtype3                                                                                 2
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           33
  subtype2                                                                                           72
  subtype3                                                                                           18
D6V32, 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)                  18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       33
                                                                                              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)                                                       0
  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"
D6V33, binary
          cls
clus        0  1
  subtype1 22 20
  subtype2 39 50
  subtype3  9  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   20
  subtype2   39   50
  subtype3    9    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        22       39        9
  PRESENT       20       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"
D6V34, continuous
D6V35, continuous
D6V36, binary
          cls
clus        0  1
  subtype1  0 16
  subtype2 46 89
  subtype3  8 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   16
  subtype2   46   89
  subtype3    8   13
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       46        8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       16       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"
D6V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          16         20
  subtype2            4          32         59
  subtype3            4           4          9
D6V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        7        4        4
  FORMER USER        16       32        4
  NEVER USED         20       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"
D6V39, continuous
D6V40, binary
          cls
clus        0  1
  subtype1 31  5
  subtype2 56 13
  subtype3 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    5
  subtype2   56   13
  subtype3   12    0
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        31       56       12
  PRESENT        5       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           0         2     0
  subtype2           3        12     0
  subtype3           0         4     1
D6V41, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       15        5 
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype2"
             clus
vv            subtype2 subtype3
  CARBOPLATIN        3        0
  CISPLATIN         12        4
  OTHER              0        1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V42, 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"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    0   6   25    7  1   4    3    3   8  0   0   3  2   0  2
  subtype2    1  21   44   20  5   5    2    6  23  1   2  13  8   0 12
  subtype3    0   9    2    4  0   1    2    1   5  0   0   1  0   1  3
D6V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A1        0        1        0
  T1B         6       21        9
  T1B1       25       44        2
  T1B2        7       20        4
  T2          1        5        0
  T2A         4        5        1
  T2A1        3        2        2
  T2A2        3        6        1
  T2B         8       23        5
  T3          0        1        0
  T3A         0        2        0
  T3B         3       13        1
  T4          2        8        0
  TIS         0        0        1
  TX          2       12        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"
D6V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        28         9
  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        29         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
D6V45, 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          5       24        8
  STAGE IB1        28       44        5
  STAGE IB2         9       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       29        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 74 25
  subtype2 61 14
  subtype3 86 30
subtype1 subtype2 subtype3 
      99       75      116 
subtype1 subtype2 subtype3 
      25       14       30 
$subtype1
TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       82.85        31.40        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       35.61        20.91        33.90        44.22        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 
       18.02        20.35         2.73        27.52         4.90       160.41 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3QD 
        1.12        58.88        50.76        16.18         8.28        13.05 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       26.40        14.50        12.82        14.89        26.79        13.91 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IR TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RL 
       14.96        13.58       113.16         0.59        16.08        47.77 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        2.24         0.10        14.70        19.79        15.55         1.22 
TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA 
       36.26         1.35         1.32         1.12         9.44       137.16 
TCGA-IR-A3LB TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q8 
       66.81        81.96         3.29        28.37        18.15        30.31 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MY-A5BD TCGA-MY-A5BE 
        7.99         0.30        13.35        20.28        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73Q 
       20.84         2.96        15.58        16.14        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       15.39        19.36        66.05        10.03        40.50        37.78 
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        50.86        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD 
       50.63        48.07        45.34        42.41        25.74        19.69 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR 
        1.71        14.53        27.25        41.42        43.27        20.09 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       14.89         4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1M5 TCGA-C5-A1MJ TCGA-C5-A1MP 
       12.39        49.48        23.67        67.46         0.46         3.58 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO 
       17.85        20.42       210.67       101.82       134.33       147.35 
TCGA-C5-A7UE TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ 
      155.77        50.99         8.35       146.86        20.81        20.91 
TCGA-C5-A901 TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1OA 
       17.03        44.94        40.04        58.88        36.76        28.90 
TCGA-DS-A1OD TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3HS 
      127.36        16.83        17.52        39.55        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD TCGA-EA-A5ZE 
       31.36        24.56        12.66         7.46        15.02        14.99 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       13.48         0.36        19.27         1.45         0.13         4.04 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX 
        0.07        20.35         7.92         2.17         1.45         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.82         3.52        25.41        10.82        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-LP-A4AU 
       14.93       147.39       117.40        96.95        78.71        11.28 
TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-Q1-A5R2 
        0.89        22.52        11.38        13.87        34.62        16.41 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A9UQ TCGA-VS-A9V2 
       93.99        12.16        31.27        36.26        35.97        14.04 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       29.26         1.41         3.91 

$subtype3
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1MH 
      177.04       173.29         5.46        19.86        46.32        38.99 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        2.43        40.93        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH 
      100.14        52.01       154.32        15.48        17.19       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ 
       94.95         9.34        13.61        45.83        99.91        23.51 
TCGA-C5-A907 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
       11.87        87.75         2.66       117.99       118.65         8.75 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HU 
       28.31        12.36        22.98        12.36        37.35        33.30 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       25.02        14.50        26.01        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB TCGA-EK-A2RD 
        6.64         1.51         0.43         0.59         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 
        0.36         1.18         0.10         0.10         0.03         6.94 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV 
        8.32        23.84         0.92        31.36         1.58         1.97 
TCGA-GH-A9DA TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
        9.01        29.85        36.36        27.42        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AX 
       20.48        15.58         8.28        21.11       195.85        12.49 
TCGA-LP-A5U3 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM 
        0.82        17.82        19.56         9.17         8.52         5.42 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-R2-A69V 
        5.49        15.95         9.04        17.56        14.07        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL 
        3.88        11.67        26.43        18.05        27.25        59.51 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       46.03        57.93        39.78        16.64         4.73        24.39 
TCGA-VS-A950 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC 
       39.78        50.14        44.94        43.40        21.30        22.72 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       46.92        40.96        15.42        26.01        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
        0.69         0.16 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  160.41   210.67   195.85 
subtype1 subtype2 subtype3 
  19.690   20.420   20.795 
[1] "0.1 - 160.4 (19.7)" "0.1 - 210.7 (20.4)" "0.0 - 195.8 (20.8)"
D7V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 50 28 10  5
  subtype2 44 16  3  1
  subtype3 46 26  8  4
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       50       44       46
  T2       28       16       26
  T3       10        3        8
  T4        5        1        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"
D7V4, binary
          cls
clus        0  1
  subtype1 45 19
  subtype2 41 21
  subtype3 47 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   19
  subtype2   41   21
  subtype3   47   19
   clus
vv  subtype1 subtype2 subtype3
  0       45       41       47
  1       19       21       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"
D7V5, binary
          cls
clus        0  1
  subtype1 37  6
  subtype2 35  1
  subtype3 43  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    6
  subtype2   35    1
  subtype3   43    3
   clus
vv  subtype1 subtype2 subtype3
  0       37       35       43
  1        6        1        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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             4                               61
  subtype2             1                               70
  subtype3             0                              122
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  17
  subtype2                                   5
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           12
  subtype2                                            2
  subtype3                                            1
D7V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    61       70      122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 17        5        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        12        2        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"
D7V7, binary
          cls
clus         0   1
  subtype1   8  94
  subtype2   8  71
  subtype3  19 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   94
  subtype2    8   71
  subtype3   19  104
     clus
vv    subtype1 subtype2 subtype3
  NO         8        8       19
  YES       94       71      104
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                         9
  subtype2                                1     7                         7
  subtype3                                6     4                        14
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    67
  subtype2                                         0    55
  subtype3                                         2    88
D7V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        6
  ASIAN                                            8        7        4
  BLACK OR AFRICAN AMERICAN                        9        7       14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           67       55       88
[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 52
  subtype2  5 50
  subtype3 12 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   52
  subtype2    5   50
  subtype3   12   67
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        5       12
  NOT HISPANIC OR LATINO       52       50       67
[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 52 16
  subtype2 37  9
  subtype3 50 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   16
  subtype2   37    9
  subtype3   50   19
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       52       37       50
  WITH TUMOR       16        9       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"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     30      3       1      2       3            58       5
  subtype2      5      2       0      6       2            58       6
  subtype3     19      0       0      4       2            95       3
D7V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              30        5       19
  CANADA               3        2        0
  NIGERIA              1        0        0
  RUSSIA               2        6        4
  UKRAINE              3        2        2
  UNITED STATES       58       58       95
  VIETNAM              5        6        3
[1] 7 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 40 42  0 11
  subtype2  8 41 27  1  1
  subtype3  2 55 49  0 12
D7V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        8        8        2
  G2       40       41       55
  G3       42       27       49
  G4        0        1        0
  GX       11        1       12
[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"
D7V16, continuous
D7V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          12
  subtype2                                           9
  subtype3                                          18
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      4
  subtype3                                      4
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             17
  subtype2                                               3             19
  subtype3                                               1             28
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  61
  subtype2                  34
  subtype3                  50
D7V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           12        9       18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        4        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        3        1
  CURRENT SMOKER                                        17       19       28
  LIFELONG NON-SMOKER                                   61       34       50
[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"
D7V19, continuous
D7V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           6       44             2        0       10
  subtype2           2       22             6        1        5
  subtype3          12       38             7        0       10
D7V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          6        2       12
  EXTERNAL            44       22       38
  EXTERNAL BEAM        2        6        7
  IMPLANTS             0        1        0
  INTERNAL            10        5       10
[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"
D7V22, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2  6  0
  subtype3 15  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2    6    0
  subtype3   15    3
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           8        6       15
  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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   7
  subtype2                  0                1                   8
  subtype3                  1                1                  23
          vv
clus       REGIONAL SITE
  subtype1            17
  subtype2             4
  subtype3            12
D7V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        7        8       23
  REGIONAL SITE             17        4       12
[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"
D7V24, binary
          cls
clus        0  1
  subtype1 24  1
  subtype2  9  0
  subtype3 25  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2    9    0
  subtype3   25    4
     clus
vv    subtype1 subtype2 subtype3
  CGY       24        9       25
  GY         1        0        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"
D7V25, continuous
D7V26, continuous
D7V27, continuous
D7V28, continuous
D7V29, continuous
D7V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       8
  subtype2                                   2                      15
  subtype3                                   4                      16
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       5
  subtype3                       0                       3
D7V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        4
  OTHER LOCATION, SPECIFY                    8       15       16
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        5        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                                             0
          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                                                                                25
  subtype3                                                                                32
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           43
  subtype2                                                                                           29
  subtype3                                                                                           52
D7V32, 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)       43
                                                                                              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)                  25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       29
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  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)       52
[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"
D7V33, binary
          cls
clus        0  1
  subtype1 24 29
  subtype2 22 28
  subtype3 25 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   29
  subtype2   22   28
  subtype3   25   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        24       22       25
  PRESENT       29       28       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"
D7V34, continuous
D7V35, continuous
D7V36, binary
          cls
clus        0  1
  subtype1  6 28
  subtype2 19 32
  subtype3 29 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   28
  subtype2   19   32
  subtype3   29   59
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            6       19       29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       28       32       59
[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"
D7V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            8          19         34
  subtype2            3          16         19
  subtype3            4          18         36
D7V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        8        3        4
  FORMER USER        19       16       18
  NEVER USED         34       19       36
[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"
D7V39, continuous
D7V40, binary
          cls
clus        0  1
  subtype1 34  7
  subtype2 33  7
  subtype3 32  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    7
  subtype2   33    7
  subtype3   32    4
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        34       33       32
  PRESENT        7        7        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           0         3     0
  subtype2           1         3     0
  subtype3           2        12     1
D7V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        2
  CISPLATIN          3        3       12
  OTHER              0        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"
D7V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        9 
 [1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype2"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    0  11   29   10  2   5    3    6  12  1   1   8  5   0  3
  subtype2    1   9   25    9  1   3    2    2   8  0   0   3  1   0  4
  subtype3    0  16   18   12  3   2    2    2  17  1   1   6  4   1 10
D7V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A1        0        1        0
  T1B        11        9       16
  T1B1       29       25       18
  T1B2       10        9       12
  T2          2        1        3
  T2A         5        3        2
  T2A1        3        2        2
  T2A2        6        2        2
  T2B        12        8       17
  T3          1        0        1
  T3A         1        0        1
  T3B         8        3        6
  T4          5        1        4
  TIS         0        0        1
  TX          3        4       10
[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"
D7V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       2        0         0         0        8        30        14
  subtype2       0        1         1         1        8        28        10
  subtype3       3        0         0         0       21        20        14
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         3          1          5        11         0
  subtype2        1         3          2          2         7         0
  subtype3        3         3          2          0        25         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          2         13         4         8
  subtype2          0         10         2         1
  subtype3          1         19         3         3
D7V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        3
  STAGE IA          0        1        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          8        8       21
  STAGE IB1        30       28       20
  STAGE IB2        14       10       14
  STAGE II          1        1        3
  STAGE IIA         3        3        3
  STAGE IIA1        1        2        2
  STAGE IIA2        5        2        0
  STAGE IIB        11        7       25
  STAGE III         0        0        1
  STAGE IIIA        2        0        1
  STAGE IIIB       13       10       19
  STAGE IVA         4        2        3
  STAGE IVB         8        1        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(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 42 15
  subtype2 76 21
  subtype3 54 15
  subtype4 18  6
  subtype5 31 12
subtype1 subtype2 subtype3 subtype4 subtype5 
      57       97       69       24       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       21       15        6       12 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 
       31.40        57.73        35.61         0.46        44.22        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH 
       33.24        17.85        20.35         2.73        20.81         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A4BA 
       58.88        50.76        16.18        17.52        14.50        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 
       14.89        26.79        47.77         2.24         0.10         7.92 
TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A57G 
       14.70        15.55         1.22         2.17         1.35         1.32 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JW-A69B 
        1.12         9.44       137.16        66.81        96.95        28.37 
TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
       30.31        13.35        15.58        16.14        15.88        15.39 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ 
       19.36        66.05        36.13        39.78        50.86         1.71 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 
       14.53        41.42        35.97        20.09        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 
        5.16         4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML 
       12.39        82.85        19.86        30.21        53.16        20.91 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI 
       83.05       100.14       154.32        15.48       131.11        94.95 
TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61        45.83         8.35       146.86        99.91        23.51 
TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-DS-A1OB TCGA-DS-A3LQ 
       20.91        17.03         4.90       160.41        28.31        22.98 
TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E 
       30.90        33.30        25.02        24.56        12.66         7.46 
TCGA-EA-A5O9 TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PM 
       13.91        13.58        12.59       113.16         1.51         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A3GN 
        0.59        16.08         0.03         0.36         0.10         0.03 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3WB 
       19.79         8.32         0.92        31.36         1.58         0.82 
TCGA-FU-A5XV TCGA-HG-A9SC TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
        1.97        10.82        81.96        24.56        21.44        20.48 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X 
        8.28        18.15         7.99         0.30         0.82        20.28 
TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       19.56         8.52        11.38         5.42        54.81        20.84 
TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-UC-A7PG TCGA-VS-A8EG 
       15.95        17.56        14.07         9.34        12.16        37.78 
TCGA-VS-A8EH TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A94Z 
       26.43        27.25        59.51        32.15        11.51        24.39 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       39.78        15.68        50.63        48.07        50.14        45.34 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UM 
       44.94        43.40        42.41        25.74        19.69        27.25 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-WL-A834 TCGA-ZJ-AAX4 
       14.53         3.42        18.25        14.89        26.01         0.69 
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        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS 
        2.66       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 
       12.36        37.35        31.53        31.36        13.05        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       14.99        13.48         0.36         1.45         0.13         4.04 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.07        20.35         1.45         3.52        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-IR-A3LL 
       20.78        14.93       147.39       117.40        29.85        36.36 
TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-Q1-A5R2 
        0.89        22.52        13.87        34.62        35.05        16.41 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-VS-A8Q9 TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A9V2 
       19.59        93.99        46.03        31.27        36.26        14.04 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       29.26         1.41         3.91 

$subtype4
TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A7X3 TCGA-C5-A8YR TCGA-DS-A0VN TCGA-DS-A1OC 
       57.04       173.29         9.34        27.52       118.65        12.36 
TCGA-EA-A410 TCGA-EA-A5ZF TCGA-EK-A2PI TCGA-EK-A2RB TCGA-EK-A2RJ TCGA-FU-A23L 
       26.40        14.96        19.27         0.07         1.18        23.84 
TCGA-FU-A3HZ TCGA-JW-A5VH TCGA-JX-A3Q0 TCGA-MA-AA41 TCGA-PN-A8MA TCGA-Q1-A6DT 
       36.26         3.29       195.85         9.17         2.96         9.04 
TCGA-VS-A8EC TCGA-VS-A94X TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UP TCGA-ZJ-A8QR 
       40.50        16.64        22.72        40.96        43.27        19.13 

$subtype5
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MQ 
       11.44        18.74       144.16         5.46        35.01        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7UC TCGA-C5-A907 
       73.18        73.45        52.01        18.02        17.19        11.87 
TCGA-DS-A1OD TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 
      127.36         8.28        14.50        26.01        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-FU-A3TX TCGA-GH-A9DA 
        6.64         0.43         0.10         6.94         1.48         9.01 
TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AX 
       78.71        27.42        15.58        21.11        11.28        12.49 
TCGA-MA-AA3Y TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI 
       17.82         5.49         3.88        11.67        10.03        18.05 
TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-AA62 
       19.96        57.93         4.73        21.30        46.92        15.42 
TCGA-ZJ-A8QQ 
       67.59 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.03     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  137.16   160.41   210.67   195.85   144.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.520   19.790   29.850   20.995   17.820 
[1] "0.1 - 137.2 (17.5)" "0.0 - 160.4 (19.8)" "0.1 - 210.7 (29.9)"
[4] "0.1 - 195.8 (21.0)" "0.1 - 144.2 (17.8)"
D8V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 34 12  2  1
  subtype2 32 28 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       34       32       47        8       19
  T2       12       28       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 31  9
  subtype2 32 22
  subtype3 38 20
  subtype4 11  2
  subtype5 21  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    9
  subtype2   32   22
  subtype3   38   20
  subtype4   11    2
  subtype5   21    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       31       32       38       11       21
  1        9       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 17  2
  subtype2 29  2
  subtype3 38  1
  subtype4 12  2
  subtype5 19  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    2
  subtype2   29    2
  subtype3   38    1
  subtype4   12    2
  subtype5   19    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       17       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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             4                               13
  subtype2             1                               98
  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                                  20
  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                                           14
  subtype2                                            0
  subtype3                                            0
  subtype4                                            1
  subtype5                                            0
D8V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    13       98       74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        14        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"
D8V7, binary
          cls
clus        0  1
  subtype1  3 55
  subtype2  7 94
  subtype3 12 62
  subtype4  3 23
  subtype5 10 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   55
  subtype2    7   94
  subtype3   12   62
  subtype4    3   23
  subtype5   10   35
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         3        7       12        3       10
  YES       55       94       62       23       35
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         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    44
  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                                            4        5        6        2
  BLACK OR AFRICAN AMERICAN                        2       13        7        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           44       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 30
  subtype2 10 52
  subtype3  3 50
  subtype4  3 16
  subtype5  4 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   30
  subtype2   10   52
  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       30       52       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 28  8
  subtype2 45 13
  subtype3 36 11
  subtype4 10  7
  subtype5 20  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    8
  subtype2   45   13
  subtype3   36   11
  subtype4   10    7
  subtype5   20    5
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       28       45       36       10       20
  WITH TUMOR        8       13       11        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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     13      3       0      1       2            37       2
  subtype2     23      0       0      5       2            67       4
  subtype3      5      2       0      5       1            57       4
  subtype4      5      0       1      1       0            17       2
  subtype5      8      0       0      0       2            33       2
D8V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  BRAZIL              13       23        5        5        8
  CANADA               3        0        2        0        0
  NIGERIA              0        0        0        1        0
  RUSSIA               1        5        5        1        0
  UKRAINE              2        2        1        0        2
  UNITED STATES       37       67       57       17       33
  VIETNAM              2        4        4        2        2
[1] 7 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 19  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
D8V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        6        4        6        0        2
  G2       27       46       39       14       10
  G3       19       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"
D8V16, continuous
D8V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           8
  subtype2                                          16
  subtype3                                           4
  subtype4                                           3
  subtype5                                           8
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      2
  subtype3                                      6
  subtype4                                      0
  subtype5                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             11
  subtype2                                               1             21
  subtype3                                               2             17
  subtype4                                               0              5
  subtype5                                               1             10
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  33
  subtype2                  45
  subtype3                  34
  subtype4                  14
  subtype5                  19
D8V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            8       16        4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        2
  CURRENT SMOKER                                        11       21       17
  LIFELONG NON-SMOKER                                   33       45       34
                                                 clus
vv                                                subtype4 subtype5
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3        8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1
  CURRENT SMOKER                                         5       10
  LIFELONG NON-SMOKER                                   14       19
[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"
D8V19, continuous
D8V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       23             0        0        5
  subtype2           4       34             3        0       14
  subtype3           7       19             5        1        1
  subtype4           1       10             2        0        1
  subtype5           5       18             5        0        4
D8V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  COMBINATION          3        4        7        1        5
  EXTERNAL            23       34       19       10       18
  EXTERNAL BEAM        0        3        5        2        5
  IMPLANTS             0        0        1        0        0
  INTERNAL             5       14        1        1        4
[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"
D8V22, 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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   4
  subtype2                  0                0                  16
  subtype3                  0                1                   6
  subtype4                  0                0                   5
  subtype5                  1                1                   7
          vv
clus       REGIONAL SITE
  subtype1             6
  subtype2            19
  subtype3             1
  subtype4             3
  subtype5             4
D8V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3 subtype4 subtype5
  DISTANT RECURRENCE         1        0        0        0        1
  LOCAL RECURRENCE           0        0        1        0        1
  PRIMARY TUMOR FIELD        4       16        6        5        7
  REGIONAL SITE              6       19        1        3        4
[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"
D8V24, binary
          cls
clus        0  1
  subtype1 10  1
  subtype2 26  1
  subtype3  5  1
  subtype4  7  0
  subtype5 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    1
  subtype2   26    1
  subtype3    5    1
  subtype4    7    0
  subtype5   10    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  CGY       10       26        5        7       10
  GY         1        1        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"
D8V25, continuous
D8V26, continuous
D8V27, continuous
D8V28, continuous
D8V29, continuous
D8V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       6
  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                       3
  subtype4                       0                       0
  subtype5                       0                       1
D8V31, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       16       23        2       10 
 [1] "subtype3" "subtype5" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype5" "subtype1" "subtype2" "subtype1"
[13] "subtype3" "subtype5" "subtype1" "subtype5" "subtype5" "subtype2"
[19] "subtype1" "subtype5" "subtype3" "subtype3" "subtype3" "subtype5"
[25] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype5"
[49] "subtype2" "subtype3" "subtype2" "subtype5" "subtype1" "subtype1"
[55] "subtype3" "subtype2" "subtype3" "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0        3        3        2
  OTHER LOCATION, SPECIFY                    6        8       16        7
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        4        3        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                                             0
          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                                                                                15
  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                                                                                           29
  subtype2                                                                                           37
  subtype3                                                                                           23
  subtype4                                                                                            9
  subtype5                                                                                           26
D8V32, 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)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       29
                                                                                              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)                                                       0
  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"
D8V33, binary
          cls
clus        0  1
  subtype1 20 15
  subtype2 17 24
  subtype3 19 29
  subtype4  5  3
  subtype5 10  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   15
  subtype2   17   24
  subtype3   19   29
  subtype4    5    3
  subtype5   10    8
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        20       17       19        5       10
  PRESENT       15       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"
D8V34, continuous
D8V35, continuous
D8V36, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2 20 46
  subtype3 20 34
  subtype4  4 12
  subtype5 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2   20   46
  subtype3   20   34
  subtype4    4   12
  subtype5   10   17
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       20       20        4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       10       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"
D8V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          13         17
  subtype2            4          17         33
  subtype3            1          14         19
  subtype4            0           5          7
  subtype5            4           4         13
D8V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        6        4        1        0        4
  FORMER USER        13       17       14        5        4
  NEVER USED         17       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"
D8V39, continuous
D8V40, binary
          cls
clus        0  1
  subtype1 27  3
  subtype2 22  5
  subtype3 32  8
  subtype4  5  2
  subtype5 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    3
  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        3        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           0         1     0
  subtype2           1         2     0
  subtype3           2         7     0
  subtype4           0         1     0
  subtype5           0         7     1
D8V41, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        3        9        1        8 
 [1] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype3"
 [7] "subtype3" "subtype5" "subtype5" "subtype2" "subtype3" "subtype5"
[13] "subtype3" "subtype3" "subtype2" "subtype5" "subtype2" "subtype5"
[19] "subtype5" "subtype3"
             clus
vv            subtype2 subtype3 subtype5
  CARBOPLATIN        1        2        0
  CISPLATIN          2        7        7
  OTHER              0        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"
D8V42, 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"
          vv
clus       T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1    0   6   23    5  1   3    3    1   4  0   0   2  1   0  2
  subtype2    0   7   14   11  3   2    0    6  17  1   2   9  6   0  7
  subtype3    1  13   26    7  0   3    1    0   7  0   0   2  1   0  4
  subtype4    0   2    3    3  1   1    1    2   4  1   0   1  1   0  2
  subtype5    0   8    6    5  1   1    2    1   5  0   0   3  1   1  2
D8V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5
  T1A1        0        0        1        0        0
  T1B         6        7       13        2        8
  T1B1       23       14       26        3        6
  T1B2        5       11        7        3        5
  T2          1        3        0        1        1
  T2A         3        2        3        1        1
  T2A1        3        0        1        1        2
  T2A2        1        6        0        2        1
  T2B         4       17        7        4        5
  T3          0        1        0        1        0
  T3A         0        2        0        0        0
  T3B         2        9        2        1        3
  T4          1        6        1        1        1
  TIS         0        0        0        0        1
  TX          2        7        4        2        2
[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"
D8V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        4        26         8
  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        17         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
D8V45, 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          4        7       13        6        7
  STAGE IB1        26       17       25        1        9
  STAGE IB2         8       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       17        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 98 25
  subtype2 56 16
  subtype3 59 25
subtype1 subtype2 subtype3 
     123       72       84 
subtype1 subtype2 subtype3 
      25       16       25 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       31.40        35.01        57.73        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
       18.02       210.67       154.32        20.35        17.19       131.11 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       13.61         2.73         8.35        99.91        23.51        27.52 
TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        4.90       160.41        11.87         1.12        58.88        50.76 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       16.18         8.28        14.50        26.40        26.01        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG 
       14.89        26.79        14.96        12.59       113.16         1.51 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN 
        0.59         1.18        47.77         2.24         0.10         0.03 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A40J 
       19.79         8.32        15.55         0.92        36.26         1.35 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LI TCGA-JW-A5VG 
        1.97         1.12         9.44       137.16        81.96        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
        8.28        18.15        30.31         7.99        11.28        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA43 
        0.30         0.82        13.35        20.28        19.56        11.38 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       54.81        35.05        20.84         5.49         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       15.95        16.14        17.56        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       19.36        66.05        10.03        40.50        37.78        26.43 
TCGA-VS-A8EJ TCGA-VS-A8EK TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       19.96        27.25        46.03        36.13        57.93        39.78 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       39.78        50.86        48.07        50.14        45.34        44.94 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UJ 
       43.40        25.74        21.30        22.72        19.69         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UV 
       14.53        27.25        41.42        43.27        20.09         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 
       18.25        67.20        18.84         5.16        14.89         4.34 
TCGA-VS-A9V5 TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       16.24         0.69         1.41 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1BF TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A3HF 
       12.39        18.74         0.46         3.58        44.22        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7X3 
       20.42       101.82       134.33        15.48       147.35         9.34 
TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-DG-A2KL 
       50.99       146.86        20.81        20.91        17.03        44.94 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ 
       58.88        36.76        16.83        17.52        39.55        37.35 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E 
       30.90        31.36        24.56        14.50        12.66         7.46 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2PI 
       15.02        14.99        13.48         0.36        26.27        19.27 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RO TCGA-EX-A1H6 
        0.59         1.45         0.13         4.04         0.07         7.92 
TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        6.94         2.17         1.45         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32        25.41        10.82        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-LP-A4AW TCGA-MU-A51Y 
      147.39        66.81       117.40        96.95         0.89        13.87 
TCGA-MU-A8JM TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QM 
        5.42        16.41        93.99        18.05        11.51        31.27 
TCGA-VS-A94W TCGA-VS-A9UQ TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZX-AA5X 
       36.26        35.97        14.04        26.01        29.26         3.91 

$subtype3
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        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-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK 
       46.32        30.21        53.16        38.99        35.61         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93        33.90        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XH TCGA-DG-A2KM 
       78.35       100.14       155.77        94.95        45.83        40.04 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA 
       87.75         2.66       117.99       118.65         8.75        28.90 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HS 
       28.31        12.36       127.36        22.98        12.36        31.53 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP 
       33.30        13.05        25.02        13.58        45.96         6.64 
TCGA-EK-A2PL TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A3GJ TCGA-FU-A23K TCGA-FU-A23L 
        0.43        16.08         0.07         0.10         1.22        23.84 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
       31.36         1.58         9.01        78.71        29.85        36.36 
TCGA-JX-A3PZ TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-Q1-A6DT 
       21.11        22.52        17.82         9.17         8.52         9.04 
TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EL TCGA-VS-A8Q8 
       14.07        19.59         3.88        11.67        59.51        32.15 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UH 
       16.64         4.73        24.39        50.63        42.41        46.92 
TCGA-VS-A9UI TCGA-VS-A9UU TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       40.96        14.53        15.42        67.59        19.13         0.16 

subtype1 subtype2 subtype3 
    0.03     0.07     0.07 
subtype1 subtype2 subtype3 
  210.67   147.39   177.04 
subtype1 subtype2 subtype3 
  19.560   17.275   30.030 
[1] "0.0 - 210.7 (19.6)" "0.1 - 147.4 (17.3)" "0.1 - 177.0 (30.0)"
D9V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 53 31 12  6
  subtype2 38 15  3  1
  subtype3 44 20  4  2
D9V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       53       38       44
  T2       31       15       20
  T3       12        3        4
  T4        6        1        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 50 16
  subtype2 41 16
  subtype3 37 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   16
  subtype2   41   16
  subtype3   37   24
   clus
vv  subtype1 subtype2 subtype3
  0       50       41       37
  1       16       16       24
[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 39  7
  subtype2 32  1
  subtype3 40  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    7
  subtype2   32    1
  subtype3   40    1
   clus
vv  subtype1 subtype2 subtype3
  0       39       32       40
  1        7        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             4                               89
  subtype2             1                               65
  subtype3             0                               87
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             2
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   7
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           13
  subtype2                                            2
  subtype3                                            0
D9V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    89       65       87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        7        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        13        2        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"
D9V7, binary
          cls
clus         0   1
  subtype1   3 124
  subtype2   6  71
  subtype3  24  63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  124
  subtype2    6   71
  subtype3   24   63
     clus
vv    subtype1 subtype2 subtype3
  NO         3        6       24
  YES      124       71       63
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                5     9                        15
  subtype2                                1     6                         3
  subtype3                                1     3                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    81
  subtype2                                         0    58
  subtype3                                         2    65
D9V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 5        1        1
  ASIAN                                            9        6        3
  BLACK OR AFRICAN AMERICAN                       15        3        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           81       58       65
[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 14 63
  subtype2  3 48
  subtype3  7 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   63
  subtype2    3   48
  subtype3    7   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        3        7
  NOT HISPANIC OR LATINO       63       48       49
[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 60 20
  subtype2 30  7
  subtype3 45 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   20
  subtype2   30    7
  subtype3   45   15
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       60       30       45
  WITH TUMOR       20        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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     35      3       1      2       4            76       6
  subtype2      7      1       0      6       2            55       6
  subtype3     11      1       0      4       0            70       1
D9V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              35        7       11
  CANADA               3        1        1
  NIGERIA              1        0        0
  RUSSIA               2        6        4
  UKRAINE              4        2        0
  UNITED STATES       76       55       70
  VIETNAM              6        6        1
[1] 7 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  6 47 59  0 13
  subtype2  8 42 24  0  2
  subtype3  2 39 33  1  8
D9V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        8        2
  G2       47       42       39
  G3       59       24       33
  G4        0        0        1
  GX       13        2        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"
D9V16, continuous
D9V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          16
  subtype2                                           7
  subtype3                                          15
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      3
  subtype3                                      3
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             18
  subtype2                                               3             18
  subtype3                                               0             25
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  71
  subtype2                  34
  subtype3                  37
D9V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           16        7       15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        3        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        3        0
  CURRENT SMOKER                                        18       18       25
  LIFELONG NON-SMOKER                                   71       34       37
[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"
D9V19, continuous
D9V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           2       57             1        0       14
  subtype2           2       20             5        0        6
  subtype3          15       22             9        1        5
D9V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          2        2       15
  EXTERNAL            57       20       22
  EXTERNAL BEAM        1        5        9
  IMPLANTS             0        0        1
  INTERNAL            14        6        5
[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"
D9V22, binary
          cls
clus        0  1
  subtype1  3  0
  subtype2  5  0
  subtype3 19  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    5    0
  subtype3   19    3
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           3        5       19
  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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                  17
  subtype2                  1                1                   9
  subtype3                  0                1                  10
          vv
clus       REGIONAL SITE
  subtype1            19
  subtype2             6
  subtype3             8
D9V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        1        0
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD       17        9       10
  REGIONAL SITE             19        6        8
[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"
D9V24, binary
          cls
clus        0  1
  subtype1 31  3
  subtype2 10  1
  subtype3 15  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    3
  subtype2   10    1
  subtype3   15    1
     clus
vv    subtype1 subtype2 subtype3
  CGY       31       10       15
  GY         3        1        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"
D9V25, continuous
D9V26, continuous
D9V27, continuous
D9V28, continuous
D9V29, continuous
D9V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       8
  subtype2                                   2                      11
  subtype3                                   4                      19
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       4
  subtype3                       0                       4
D9V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        4
  OTHER LOCATION, SPECIFY                    8       11       19
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        4        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                                             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                                                                                30
  subtype2                                                                                22
  subtype3                                                                                25
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           51
  subtype2                                                                                           30
  subtype3                                                                                           38
D9V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     15
  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)       51
                                                                                              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)                  22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              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)                  25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       38
[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"
D9V33, binary
          cls
clus        0  1
  subtype1 23 23
  subtype2 23 23
  subtype3 22 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   23
  subtype2   23   23
  subtype3   22   27
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       23       22
  PRESENT       23       23       27
[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"
D9V34, continuous
D9V35, continuous
D9V36, binary
          cls
clus        0  1
  subtype1  9 44
  subtype2 18 30
  subtype3 24 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   44
  subtype2   18   30
  subtype3   24   39
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            9       18       24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       44       30       39
[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"
D9V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          21         44
  subtype2            4          16         17
  subtype3            5          16         23
D9V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        6        4        5
  FORMER USER        21       16       16
  NEVER USED         44       17       23
[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"
D9V39, continuous
D9V40, binary
          cls
clus        0  1
  subtype1 29  4
  subtype2 30  5
  subtype3 36  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    4
  subtype2   30    5
  subtype3   36    9
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        29       30       36
  PRESENT        4        5        9
[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         2     0
  subtype2           0         2     1
  subtype3           3        13     0
D9V41, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        3       16 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2"
             clus
vv            subtype2 subtype3
  CARBOPLATIN        0        3
  CISPLATIN          2       13
  OTHER              1        0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V42, continuous
          vv
clus       T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1  12   27   14  3   6    2    5  15  1   2   9  6   1  8
  subtype2   6   22   10  0   4    3    2   6  0   0   3  1   0  6
  subtype3  17   21    6  3   0    2    2  13  0   0   4  2   0  3
D9V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1B        12        6       17
  T1B1       27       22       21
  T1B2       14       10        6
  T2          3        0        3
  T2A         6        4        0
  T2A1        2        3        2
  T2A2        5        2        2
  T2B        15        6       13
  T3          1        0        0
  T3A         2        0        0
  T3B         9        3        4
  T4          6        1        2
  TIS         1        0        0
  TX          8        6        3
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       3        0         0        9        35        17        2
  subtype2       0        1         1        5        24        12        2
  subtype3       2        0         0       22        17         7        1
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIA STAGE IIIB
  subtype1         4          0          4        18          3         16
  subtype2         3          3          2         8          0          9
  subtype3         1          2          1        15          0         16
          vv
clus       STAGE IVA STAGE IVB
  subtype1         3         9
  subtype2         3         1
  subtype3         2         1
D9V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        2
  STAGE IA          0        1        0
  STAGE IA2         0        1        0
  STAGE IB          9        5       22
  STAGE IB1        35       24       17
  STAGE IB2        17       12        7
  STAGE II          2        2        1
  STAGE IIA         4        3        1
  STAGE IIA1        0        3        2
  STAGE IIA2        4        2        1
  STAGE IIB        18        8       15
  STAGE IIIA        3        0        0
  STAGE IIIB       16        9       16
  STAGE IVA         3        3        2
  STAGE IVB         9        1        1
[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  45  15
  subtype2  37   9
  subtype3  19  12
  subtype4 112  30
subtype1 subtype2 subtype3 subtype4 
      60       46       31      142 
subtype1 subtype2 subtype3 subtype4 
      15        9       12       30 
$subtype1
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       57.73         0.46        44.22        38.43        33.24        17.85 
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        58.88        50.76 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       16.18        17.52        26.40        14.50        12.82        14.89 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 
       14.96         0.59        47.77         2.24         0.10         7.92 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 
        2.17        36.26         1.35         1.32         1.12         9.44 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B 
      137.16        66.81        96.95        81.96         3.29        28.37 
TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV 
       30.31        13.35        54.81         2.96        15.58        16.14 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH 
       15.88        15.39        66.05        19.96        36.13        39.78 
TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       50.86         1.71        14.53        41.42        43.27        35.97 
TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 
       20.09        67.20        18.84         5.16         4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
       12.39        20.42       101.82       134.33        15.48       147.35 
TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8ZZ TCGA-DG-A2KL TCGA-DS-A5RQ TCGA-EA-A1QS 
       50.99       146.86        20.91        44.94        16.83        39.55 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E 
       30.90        31.53        31.36        24.56        12.66         7.46 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PM 
       15.02        14.99        13.48         0.36        19.27         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RO TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HG-A9SC 
        0.13         4.04         0.07         1.45        25.41        10.82 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-LP-A4AW TCGA-MA-AA3W 
       21.67        20.78        14.93       147.39         0.89        22.52 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8Q8 
       13.87         5.42        16.41        93.99        18.05        32.15 
TCGA-VS-A8QM TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZX-AA5X 
       31.27        14.04        29.26         3.91 

$subtype3
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        23.67        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        3.58        33.90        87.75        58.88        36.76         2.66 
TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT TCGA-FU-A23K 
       28.90        28.31        12.36       127.36        12.36         1.22 
TCGA-FU-A23L 
       23.84 

$subtype4
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A1MN TCGA-C5-A2LT 
       57.04        11.44        18.74        19.86        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05        78.35       100.14        52.01        18.02 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      210.67       154.32        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
        9.34        13.61        45.83         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 TCGA-DG-A2KM 
       27.52        17.03         4.90       160.41        11.87        40.04 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ 
      117.99       118.65         8.75        22.98         8.28        37.35 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EA-A5FO 
       33.30        13.05        25.02        14.50        26.01        26.79 
TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2IR 
       13.58        12.59        45.96        26.27         6.64       113.16 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RJ 
        1.51         0.43         1.45        16.08         0.07         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        0.10         0.03         6.94        19.79         8.32        15.55 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92        31.36         1.58         1.48         0.82         3.52 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
        1.97         9.01       117.40        78.71        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       27.42        24.56        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
       18.15        21.11         7.99        11.28        12.49         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.82        20.28        17.82        19.56         9.17         8.52 
TCGA-MA-AA43 TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       11.38        35.05        20.84         5.49        15.95         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       17.56        14.07         9.34        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EK 
       11.67        10.03        40.50        37.78        26.43        27.25 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X 
       59.51        46.03        11.51        57.93        36.26        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        24.39        39.78        50.63        48.07        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       45.34        44.94        43.40        42.41        25.74        21.30 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU 
       22.72        19.69        46.92        40.96        27.25        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
        3.42        18.25        14.89        15.42        26.01        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       19.13         0.69         1.41         0.16 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     1.22     0.03 
subtype1 subtype2 subtype3 subtype4 
  137.16   147.39   177.04   210.67 
subtype1 subtype2 subtype3 subtype4 
  17.685   18.660   35.610   19.640 
[1] "0.1 - 137.2 (17.7)" "0.1 - 147.4 (18.7)" "1.2 - 177.0 (35.6)"
[4] "0.0 - 210.7 (19.6)"
D10V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 32 18  2  2
  subtype2 26  8  3  1
  subtype3 18  5  1  0
  subtype4 59 35 13  6
D10V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       32       26       18       59
  T2       18        8        5       35
  T3        2        3        1       13
  T4        2        1        0        6
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus        0  1
  subtype1 34  8
  subtype2 25 11
  subtype3 13 11
  subtype4 56 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    8
  subtype2   25   11
  subtype3   13   11
  subtype4   56   26
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       34       25       13       56
  1        8       11       11       26
[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"
D10V5, binary
          cls
clus        0  1
  subtype1 21  4
  subtype2 24  1
  subtype3 15  0
  subtype4 51  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2   24    1
  subtype3   15    0
  subtype4   51    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       21       24       15       51
  1        4        1        0        4
[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                               16
  subtype2             1                               49
  subtype3             0                               30
  subtype4             1                              146
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             0
  subtype3                                             0
  subtype4                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  20
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           15
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
D10V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    16       49       30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20        0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        15        0        0
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        1
  CERVICAL SQUAMOUS CELL CARCINOMA                   146
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1
  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"
D10V7, binary
          cls
clus         0   1
  subtype1   1  61
  subtype2   3  47
  subtype3  19  12
  subtype4  10 138
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   61
  subtype2    3   47
  subtype3   19   12
  subtype4   10  138
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        3       19       10
  YES       61       47       12      138
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                1     5                         2
  subtype3                                0     2                         3
  subtype4                                5     6                        19
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    44
  subtype2                                         0    35
  subtype3                                         0    26
  subtype4                                         2    99
D10V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        0        5
  ASIAN                                            5        5        2        6
  BLACK OR AFRICAN AMERICAN                        3        2        3       19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           44       35       26       99
[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"
D10V11, binary
          cls
clus        0  1
  subtype1  6 32
  subtype2  3 31
  subtype3  1 22
  subtype4 14 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   32
  subtype2    3   31
  subtype3    1   22
  subtype4   14   75
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            6        3        1       14
  NOT HISPANIC OR LATINO       32       31       22       75
[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"
D10V12, continuous
D10V13, binary
          cls
clus        0  1
  subtype1 29  9
  subtype2 22  4
  subtype3 16 10
  subtype4 68 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    9
  subtype2   22    4
  subtype3   16   10
  subtype4   68   19
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       29       22       16       68
  WITH TUMOR        9        4       10       19
[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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     15      3       1      2       1            37       3
  subtype2      5      1       0      6       2            31       5
  subtype3      0      0       0      1       0            30       0
  subtype4     33      1       0      3       3           103       5
D10V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  BRAZIL              15        5        0       33
  CANADA               3        1        0        1
  NIGERIA              1        0        0        0
  RUSSIA               2        6        1        3
  UKRAINE              1        2        0        3
  UNITED STATES       37       31       30      103
  VIETNAM              3        5        0        5
[1] 7 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  6 28 22  0  6
  subtype2  5 28 14  0  2
  subtype3  0 17 14  0  0
  subtype4  5 55 66  1 15
D10V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        6        5        0        5
  G2       28       28       17       55
  G3       22       14       14       66
  G4        0        0        0        1
  GX        6        2        0       15
[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"
D10V16, continuous
D10V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  subtype2                                           3
  subtype3                                           8
  subtype4                                          20
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
  subtype4                                      3
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             11
  subtype2                                               2             11
  subtype3                                               0              5
  subtype4                                               2             34
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  37
  subtype2                  22
  subtype3                  14
  subtype4                  69
D10V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        3        8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        0
  CURRENT SMOKER                                        11       11        5
  LIFELONG NON-SMOKER                                   37       22       14
                                                 clus
vv                                                subtype4
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        2
  CURRENT SMOKER                                        34
  LIFELONG NON-SMOKER                                   69
[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"
D10V19, continuous
D10V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           1       27             0        0        4
  subtype2           0       14             3        0        4
  subtype3          13        1             7        1        0
  subtype4           5       57             5        0       17
D10V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  COMBINATION          1        0       13        5
  EXTERNAL            27       14        1       57
  EXTERNAL BEAM        0        3        7        5
  IMPLANTS             0        0        1        0
  INTERNAL             4        4        0       17
[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"
D10V22, binary
          cls
clus        0  1
  subtype1  1  0
  subtype2  2  0
  subtype3 17  1
  subtype4  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    0
  subtype2    2    0
  subtype3   17    1
  subtype4    7    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           1        2       17        7
  TREATMENT NOT COMPLETED        0        0        1        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   6
  subtype2                  0                1                   5
  subtype3                  0                0                   2
  subtype4                  1                1                  23
          vv
clus       REGIONAL SITE
  subtype1             5
  subtype2             4
  subtype3             0
  subtype4            24
D10V23, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      12       10        2       49 
 [1] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype2" "subtype4" "subtype4" "subtype1" "subtype2" "subtype4"
[19] "subtype4" "subtype2" "subtype1" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype1" "subtype2" "subtype2" "subtype1" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[37] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
[49] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[55] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype1"
[61] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[67] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
                     clus
vv                    subtype1 subtype2 subtype4
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        6        5       23
  REGIONAL SITE              5        4       24
[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"
D10V24, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2  6  1
  subtype3  2  0
  subtype4 36  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2    6    1
  subtype3    2    0
  subtype4   36    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  CGY       12        6        2       36
  GY         0        1        0        4
[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"
D10V25, continuous
D10V26, continuous
D10V27, continuous
D10V28, continuous
D10V29, continuous
D10V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       6
  subtype2                                   1                       6
  subtype3                                   2                      14
  subtype4                                   3                      12
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       1
  subtype3                       0                       2
  subtype4                       0                       5
D10V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        2        3
  OTHER LOCATION, SPECIFY                    6        6       14       12
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        1        2        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                                             0
  subtype3                                             2
  subtype4                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              7
  subtype2                                              4
  subtype3                                              1
  subtype4                                             13
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                16
  subtype2                                                                                15
  subtype3                                                                                12
  subtype4                                                                                34
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           29
  subtype2                                                                                           18
  subtype3                                                                                           14
  subtype4                                                                                           58
D10V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      7
  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)       29
                                                                                              clus
vv                                                                                             subtype2
  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)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       18
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  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)       14
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     13
  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)       58
[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"
D10V33, binary
          cls
clus        0  1
  subtype1 20 15
  subtype2 14 15
  subtype3  6 18
  subtype4 28 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   15
  subtype2   14   15
  subtype3    6   18
  subtype4   28   25
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        20       14        6       28
  PRESENT       15       15       18       25
[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"
D10V34, continuous
D10V35, continuous
D10V36, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2 14 21
  subtype3  9 12
  subtype4 28 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2   14   21
  subtype3    9   12
  subtype4   28   69
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       14        9       28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       11       21       12       69
[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"
D10V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          13         20
  subtype2            0          10         11
  subtype3            0           5         10
  subtype4            8          25         43
D10V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        7        0        0        8
  FORMER USER        13       10        5       25
  NEVER USED         20       11       10       43
[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"
D10V39, continuous
D10V40, binary
          cls
clus        0  1
  subtype1 27  4
  subtype2 18  4
  subtype3 17  6
  subtype4 33  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    4
  subtype2   18    4
  subtype3   17    6
  subtype4   33    4
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        27       18       17       33
  PRESENT        4        4        6        4
[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           0         0     0
  subtype2           0         1     0
  subtype3           3         9     0
  subtype4           0         7     1
D10V41, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 subtype4 
       1       12        8 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
[19] "subtype4" "subtype4"
             clus
vv            subtype3 subtype4
  CARBOPLATIN        3        0
  CISPLATIN          9        7
  OTHER              0        1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        6        3        6 
 [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype2" "subtype4"
 [7] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[13] "subtype2" "subtype4" "subtype2"
          vv
clus       T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3A T3B T4 TIS TX
  subtype1   6   20    6  1   4    2    3   8  0   0   2  2   0  2
  subtype2   7   14    5  0   3    1    1   3  0   0   3  1   0  3
  subtype3   6    9    3  1   0    1    0   3  0   0   1  0   0  0
  subtype4  16   27   16  4   3    3    5  20  1   2  10  6   1 12
D10V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4
  T1B         6        7        6       16
  T1B1       20       14        9       27
  T1B2        6        5        3       16
  T2          1        0        1        4
  T2A         4        3        0        3
  T2A1        2        1        1        3
  T2A2        3        1        0        5
  T2B         8        3        3       20
  T3          0        0        0        1
  T3A         0        0        0        2
  T3B         2        3        1       10
  T4          2        1        0        6
  TIS         0        0        0        1
  TX          2        3        0       12
[1] 14  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       1        0         0        5        23         9        1
  subtype2       0        1         1        4        17         5        1
  subtype3       0        0         0       12         5         4        0
  subtype4       4        0         0       15        31        18        3
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIA STAGE IIIB
  subtype1         3          1          2         7          0          5
  subtype2         2          1          1         6          0          7
  subtype3         1          1          0         2          0          6
  subtype4         2          2          4        26          3         23
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         4
  subtype2         2         1
  subtype3         0         0
  subtype4         5         6
D10V45, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        0        0        4
  STAGE IA          0        1        0        0
  STAGE IA2         0        1        0        0
  STAGE IB          5        4       12       15
  STAGE IB1        23       17        5       31
  STAGE IB2         9        5        4       18
  STAGE II          1        1        0        3
  STAGE IIA         3        2        1        2
  STAGE IIA1        1        1        1        2
  STAGE IIA2        2        1        0        4
  STAGE IIB         7        6        2       26
  STAGE IIIA        0        0        0        3
  STAGE IIIB        5        7        6       23
  STAGE IVA         1        2        0        5
  STAGE IVB         4        1        0        6
[1] 15  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
