[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPAPOBEC"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "APOBEC"
[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/APOBEC_Pipelines/CESC-TP/15165229/APOBEC_clinical_corr_input_15168231/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=304, in cluster file=194, common to both=194
[1]   2 194
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  44   41  109 
   0 HIGH  LOW 
  44   41  109 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          144            40            10 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          144            40            10 
[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 194 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=39,	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=144,	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=13,	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=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	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=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=66,	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=5,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=22,	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=27,	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=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	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=7,	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"
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "6"                                                                                                                                
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NO PELVIC SPREAD PELVIC SPREAD
freq.values   "1"                       "1"              "1"          
freq.contrast "6"                       "6"              "6"          
both >= 3     "FALSE"                   "FALSE"          "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "6"                                                                         
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 "6"                                                                                                                                       
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "6"                                                                      
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=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'LYMPH_NODES_EXAMINED':	nDistinctValues=47,	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=31,	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=10,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 58:'AGE_AT_DIAGNOSIS':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 59:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	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 194 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=57, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
104  40   3   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  104    40     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
104  40   3   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  104    40     5 
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=28, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=66, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=18, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=22, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=27, 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=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=4, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, 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=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=47, 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=31, 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=10, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=13, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=57, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2   0  1
  0    33 10
  HIGH 32  6
  LOW  85 24
   0 HIGH  LOW 
  43   38  109 
   0 HIGH  LOW 
  10    6   24 
$`0`
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M2 
       67.46        57.73        73.18        73.45        78.35        33.24 
TCGA-C5-A7CG TCGA-C5-A7CM TCGA-DG-A2KJ TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF 
      210.67        20.35        58.88        28.90        22.98        16.18 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5O9 
        8.28        12.36        26.40        12.82        14.89        13.91 
TCGA-EA-A5ZD TCGA-EK-A2R9 TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EX-A1H5 TCGA-EX-A449 
       15.02         0.13         0.36        47.77        20.35        14.70 
TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-HG-A2PA 
        8.32         2.17        36.26         1.58         1.32        25.41 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-JW-A5VG TCGA-JW-A5VH 
       21.67         9.44       147.39       117.40        27.42         3.29 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-Q1-A6DV TCGA-Q1-A73R 
       20.48        28.37        30.31         7.99        16.14        15.39 
TCGA-Q1-A73S 
       19.36 

$HIGH
TCGA-C5-A1BL TCGA-C5-A1BQ TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HE 
      173.29        19.86        38.99         2.43       100.14        18.02 
TCGA-C5-A7UH TCGA-DG-A2KK TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-EA-A3HU TCGA-EK-A2H0 
      131.11        50.76        58.88       117.99        33.30        45.96 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC 
        1.51         0.43         0.59         1.45        16.08         4.04 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-FU-A3HY TCGA-IR-A3LA 
        0.03         1.18         0.10         0.10        31.36       137.16 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VL 
       78.71        81.96        29.85        36.36        21.44        15.58 
TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73O 
      195.85         0.30        13.87        54.81        16.41        14.07 
TCGA-Q1-A73P TCGA-UC-A7PF 
       15.88        93.99 

$LOW
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 
       36.56       144.16       177.04        82.85         5.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       46.32        30.21        35.01        53.16        35.61         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LX 
       20.91        40.93         3.58        33.90        44.22        83.05 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       38.43        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 
      134.33        15.48       147.35        17.19       155.77         9.34 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
        1.12        44.94        40.04        87.75        36.76         2.66 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
      118.65        16.83        17.52        39.55        37.35        30.90 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 
       31.36        13.05        25.02        14.50        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A5ZF 
       26.01        12.66         7.46        26.79        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.58        13.48        12.59        26.27         6.64        19.27 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        0.59         0.07         2.24         0.10         0.07         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92         6.94        19.79         1.22        23.84         0.92 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
        1.45         1.48         0.82         3.52         1.35         1.97 
TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JW-A5VI 
        1.12        20.78        14.93        66.81        96.95        24.56 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
        8.28        21.11        11.28         0.89        12.49         0.82 
TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       13.35        34.62        35.05        20.84        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.04        17.56         9.34        19.59         3.88        11.67 
TCGA-WL-A834 
       26.01 

   0 HIGH  LOW 
0.13 0.03 0.03 
     0   HIGH    LOW 
210.67 195.85 177.04 
    0  HIGH   LOW 
20.35 20.65 18.74 
[1] "0.1 - 210.7 (20.4)" "0.0 - 195.8 (20.6)" "0.0 - 177.0 (18.7)"
D1V2, continuous
      vv
clus   T1 T2 T3+T4
  0    29  9     2
  HIGH 17  9     1
  LOW  58 22     2
D1V3, multiclass
       clus
vv       0 HIGH LOW
  T1    29   17  58
  T2     9    9  22
  T3+T4  2    1   2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
      cls
clus    0  1
  0    25 10
  HIGH 18  7
  LOW  52 27
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      25   10
  HIGH   18    7
  LOW    52   27
   clus
vv   0 HIGH LOW
  0 25   18  52
  1 10    7  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"
D1V5, binary
      cls
clus    0  1
  0    20  3
  HIGH 13  1
  LOW  46  0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      20    3
  HIGH   13    1
  LOW    46    0
   clus
vv   0 HIGH LOW
  0 20   13  46
  1  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"
      vv
clus   ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  0                3                               28
  HIGH             0                               35
  LOW              1                               95
      vv
clus   ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  0                                                1
  HIGH                                             1
  LOW                                              3
      vv
clus   ENDOCERVICAL TYPE OF ADENOCARCINOMA
  0                                     10
  HIGH                                   4
  LOW                                    8
      vv
clus   ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  0                                            1
  HIGH                                         1
  LOW                                          0
      vv
clus   MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  0                                               1
  HIGH                                            0
  LOW                                             2
D1V6, multiclass
                                               clus
vv                                               0 HIGH LOW
  ADENOSQUAMOUS                                  3    0   1
  CERVICAL SQUAMOUS CELL CARCINOMA              28   35  95
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE  1    1   3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA           10    4   8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX      1    1   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE   1    0   2
[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
  0     6 38
  HIGH  5 36
  LOW  21 88
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       6   38
  HIGH    5   36
  LOW    21   88
     clus
vv     0 HIGH LOW
  NO   6    5  21
  YES 38   36  88
[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
  0                                   2     4                         6
  HIGH                                3     2                         3
  LOW                                 3    13                         7
      vv
clus   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  0                                            0    29
  HIGH                                         1    27
  LOW                                          0    82
D1V10, multiclass
                                           clus
vv                                           0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE           2    3   3
  ASIAN                                      4    2  13
  BLACK OR AFRICAN AMERICAN                  6    3   7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER  0    1   0
  WHITE                                     29   27  82
[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
  0     5 33
  HIGH  6 21
  LOW   3 80
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   33
  HIGH    6   21
  LOW     3   80
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      5    6   3
  NOT HISPANIC OR LATINO 33   21  80
[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
  0    27  8
  HIGH 19  6
  LOW  51 17
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      27    8
  HIGH   19    6
  LOW    51   17
            clus
vv            0 HIGH LOW
  TUMOR FREE 27   19  51
  WITH TUMOR  8    6  17
[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   CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  0         1      3       2            37       1
  HIGH      1      1       0            37       2
  LOW       3      6       4            85      11
D1V14, multiclass
               clus
vv               0 HIGH LOW
  CANADA         1    1   3
  RUSSIA         3    1   6
  UKRAINE        2    0   4
  UNITED STATES 37   37  85
  VIETNAM        1    2  11
[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   G1 G2 G3 G4 GX
  0     2 20 20  0  2
  HIGH  3 14 21  1  1
  LOW   9 54 41  0  5
D1V15, multiclass
    clus
vv    0 HIGH LOW
  G1  2    3   9
  G2 20   14  54
  G3 20   21  41
  G4  0    1   0
  GX  2    1   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"
D1V16, continuous
D1V17, continuous
      vv
clus   CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  0                                              6
  HIGH                                           6
  LOW                                           14
      vv
clus   CURRENT REFORMED SMOKER FOR > 15 YEARS
  0                                         2
  HIGH                                      1
  LOW                                       5
      vv
clus   CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  0                                                  0              9
  HIGH                                               0              4
  LOW                                                1             24
      vv
clus   LIFELONG NON-SMOKER
  0                     20
  HIGH                  19
  LOW                   54
D1V18, multiclass
                                                 clus
vv                                                 0 HIGH LOW
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS      6    6  14
  CURRENT REFORMED SMOKER FOR > 15 YEARS           2    1   5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED  0    0   1
  CURRENT SMOKER                                   9    4  24
  LIFELONG NON-SMOKER                             20   19  54
[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 IMPLANTS INTERNAL
  0              2       13             3        1        1
  HIGH           3       14             2        0        1
  LOW           15       27             7        0        5
D1V21, multiclass
               clus
vv               0 HIGH LOW
  COMBINATION    2    3  15
  EXTERNAL      13   14  27
  EXTERNAL BEAM  3    2   7
  IMPLANTS       1    0   0
  INTERNAL       1    1   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"
D1V22, binary
      cls
clus    0  1
  0     5  0
  HIGH  3  2
  LOW  18  1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5    0
  HIGH    3    2
  LOW    18    1
                         clus
vv                         0 HIGH LOW
  COMPLETED AS PLANNED     5    3  18
  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 REGIONAL SITE
  0                     1                1                   4             0
  HIGH                  0                0                   5             1
  LOW                   1                1                  11             3
D1V23, multiclass
                     clus
vv                     0 HIGH LOW
  DISTANT RECURRENCE   1    0   1
  LOCAL RECURRENCE     1    0   1
  PRIMARY TUMOR FIELD  4    5  11
  REGIONAL SITE        0    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"
D1V24, binary
      cls
clus   0 1
  0    6 0
  HIGH 3 0
  LOW  7 4
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       6    0
  HIGH    3    0
  LOW     7    4
     clus
vv    0 HIGH LOW
  CGY 6    3   7
  GY  0    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"
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, continuous
      vv
clus   MACROSCOPIC PARAMETRIAL INVOLVEMENT MICROSCOPIC PARAMETRIAL INVOLVEMENT
  0                                      1                                   1
  HIGH                                   0                                   2
  LOW                                    1                                   4
      vv
clus   OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  0                          7                       0                       1
  HIGH                       3                       0                       1
  LOW                       18                       1                       4
D1V31, multiclass
                                     clus
vv                                     0 HIGH LOW
  MACROSCOPIC PARAMETRIAL INVOLVEMENT  1    0   1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT  1    2   4
  OTHER LOCATION, SPECIFY              7    3  18
  POSITIVE BLADDER MARGIN              0    0   1
  POSITIVE VAGINAL MARGIN              1    1   4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  0                                                1
  HIGH                                             0
  LOW                                              1
      vv
clus   PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  0                                                 0
  HIGH                                              1
  LOW                                               9
      vv
clus   POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  0                                                                                    8
  HIGH                                                                                19
  LOW                                                                                 33
      vv
clus   PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  0                                                                                              29
  HIGH                                                                                           12
  LOW                                                                                            47
D1V32, multiclass
                                                                                              clus
vv                                                                                              0
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                0
  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) 29
                                                                                              clus
vv                                                                                             HIGH
  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)              19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)   12
                                                                                              clus
vv                                                                                             LOW
  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)             33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)  47
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V33, binary
      cls
clus    0  1
  0    16 16
  HIGH 10 14
  LOW  37 37
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      16   16
  HIGH   10   14
  LOW    37   37
         clus
vv         0 HIGH LOW
  ABSENT  16   10  37
  PRESENT 16   14  37
[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
  0     5 23
  HIGH  8 17
  LOW  26 46
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   23
  HIGH    8   17
  LOW    26   46
                                          clus
vv                                          0 HIGH LOW
  KERATINIZING SQUAMOUS CELL CARCINOMA      5    8  26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 23   17  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"
D1V37, continuous
      vv
clus   CURRENT USER FORMER USER NEVER USED
  0               3          11         16
  HIGH            1           7          8
  LOW             4          25         22
D1V38, multiclass
              clus
vv              0 HIGH LOW
  CURRENT USER  3    1   4
  FORMER USER  11    7  25
  NEVER USED   16    8  22
[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
  0    24  5
  HIGH 16  4
  LOW  48  7
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      24    5
  HIGH   16    4
  LOW    48    7
         clus
vv         0 HIGH LOW
  ABSENT  24   16  48
  PRESENT  5    4   7
[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
  0              1         4     0
  HIGH           1         3     0
  LOW            0         9     1
D1V41, multiclass
             clus
vv            0 HIGH LOW
  CARBOPLATIN 1    1   0
  CISPLATIN   4    3   9
  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"
D1V42, continuous
[1] "Remove cluster labels:" "0"                      "HIGH"                  
clus
   0 HIGH  LOW 
   1    2    7 
TCGA-C5-A1BN TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-EK-A2RO TCGA-HM-A3JK 
       "LOW"        "LOW"        "LOW"        "LOW"        "LOW"        "LOW" 
TCGA-JW-A852 
       "LOW" 
      vv
clus   T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  0       0   6   15    8  0   2    0    4   3  0   1  1  1
  HIGH    0   2    9    6  0   1    2    2   4  1   0  0  2
  LOW     1  13   36    8  4   4    4    4   6  0   1  1  6
D1V43, multiclass
      clus
vv      0 HIGH LOW
  T1A1  0    0   1
  T1B   6    2  13
  T1B1 15    9  36
  T1B2  8    6   8
  T2    0    0   4
  T2A   2    1   4
  T2A1  0    2   4
  T2A2  4    2   4
  T2B   3    4   6
  T3    0    1   0
  T3B   1    0   1
  T4    1    0   1
  TX    1    2   6
[1] 13  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
  0          1        0         0         0        7        13        10
  HIGH       0        0         0         1        3         8         7
  LOW        3        1         1         0       18        32        12
      vv
clus   STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  0           0         2          0          3         2         0          3
  HIGH        1         1          2          1         4         1          9
  LOW         3         3          3          3         8         0         17
      vv
clus   STAGE IVA STAGE IVB
  0            0         3
  HIGH         0         1
  LOW          2         1
D1V45, multiclass
            clus
vv            0 HIGH LOW
  STAGE I     1    0   3
  STAGE IA    0    0   1
  STAGE IA1   0    0   1
  STAGE IA2   0    1   0
  STAGE IB    7    3  18
  STAGE IB1  13    8  32
  STAGE IB2  10    7  12
  STAGE II    0    1   3
  STAGE IIA   2    1   3
  STAGE IIA1  0    2   3
  STAGE IIA2  3    1   3
  STAGE IIB   2    4   8
  STAGE III   0    1   0
  STAGE IIIB  3    9  17
  STAGE IVA   0    0   2
  STAGE IVB   3    1   1
[1] 16  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 = APOBEC_ENRICH
D2V1, survival
               sevent
clus2             0   1
  FC.HIGH.SIG   111  30
  FC.LOW.NONSIG  29  10
  FC.NEUTRAL     10   0
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          141            39            10 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           30            10             0 
$FC.HIGH.SIG
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       19.86        31.40        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        33.90        44.22        83.05       100.14        38.43 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
      134.33        15.48       147.35        17.19       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH 
       36.76         2.66       117.99       118.65        16.83        17.52 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
       39.55        37.35        30.90        31.36        33.30        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       25.02        14.50        24.56        14.50        26.01        12.66 
TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
        7.46        14.99        14.96        13.58        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51        19.27         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45        16.08         0.07         4.04         0.03 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
        0.03         7.92         6.94        19.79         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92        31.36         1.45         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.35         1.97         1.12        14.93       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
       96.95        78.71        81.96        29.85        36.36        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU 
       21.44        15.58         8.28        21.11       195.85        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
       12.49         0.30         0.82        13.35        13.87        34.62 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       54.81        20.84        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 
       17.56        14.07        15.88         9.34        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

$FC.LOW.NONSIG
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CM 
       67.46        57.73        78.35        33.24       210.67        20.35 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 
       28.90        22.98        16.18         8.28        12.36        26.40 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2R9 TCGA-EK-A2RE 
       12.82        14.89        13.91        15.02         0.13         0.36 
TCGA-EK-A2RL TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3HZ 
       47.77        20.35        14.70         8.32         2.17        36.26 
TCGA-FU-A3TQ TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LC 
        1.58         1.32        25.41        21.67         9.44       117.40 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
       27.42         3.29        20.48        28.37        30.31         7.99 
TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        15.39        19.36 

$FC.NEUTRAL
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7UE TCGA-DG-A2KJ TCGA-EA-A5FO TCGA-EK-A2GZ 
       73.18        73.45       155.77        58.88        26.79        12.59 
TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-LP-A4AW TCGA-MY-A5BE 
       20.78       147.39         0.89        35.05 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.03          0.13          0.89 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       195.85        210.67        155.77 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       18.740        19.360        46.965 
[1] "0.0 - 195.8 (18.7)" "0.1 - 210.7 (19.4)" "0.9 - 155.8 (47.0)"
D2V2, continuous
               vv
clus            T1 T2 T3+T4
  FC.HIGH.SIG   72 30     3
  FC.LOW.NONSIG 25  9     2
  FC.NEUTRAL     7  1     0
D2V3, multiclass
       clus
vv      FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1             72            25          7
  T2             30             9          1
  T3+T4           3             2          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"
D2V4, binary
               cls
clus             0  1
  FC.HIGH.SIG   67 33
  FC.LOW.NONSIG 23  8
  FC.NEUTRAL     5  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     67   33
  FC.LOW.NONSIG   23    8
  FC.NEUTRAL       5    3
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0          67            23          5
  1          33             8          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"
D2V5, binary
               cls
clus             0  1
  FC.HIGH.SIG   57  1
  FC.LOW.NONSIG 17  3
  FC.NEUTRAL     5  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     57    1
  FC.LOW.NONSIG   17    3
  FC.NEUTRAL       5    0
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0          57            17          5
  1           1             3          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            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  FC.HIGH.SIG               1                              124
  FC.LOW.NONSIG             3                               24
  FC.NEUTRAL                0                               10
               vv
clus            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  FC.HIGH.SIG                                               4
  FC.LOW.NONSIG                                             1
  FC.NEUTRAL                                                0
               vv
clus            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  FC.HIGH.SIG                                    12
  FC.LOW.NONSIG                                  10
  FC.NEUTRAL                                      0
               vv
clus            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  FC.HIGH.SIG                                           1
  FC.LOW.NONSIG                                         1
  FC.NEUTRAL                                            0
               vv
clus            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  FC.HIGH.SIG                                              2
  FC.LOW.NONSIG                                            1
  FC.NEUTRAL                                               0
D2V6, multiclass
                                               clus
vv                                              FC.HIGH.SIG FC.LOW.NONSIG
  ADENOSQUAMOUS                                           1             3
  CERVICAL SQUAMOUS CELL CARCINOMA                      124            24
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE           4             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                    12            10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX               1             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE            2             1
                                               clus
vv                                              FC.NEUTRAL
  ADENOSQUAMOUS                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                      10
  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 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
               cls
clus              0   1
  FC.HIGH.SIG    25 119
  FC.LOW.NONSIG   5  35
  FC.NEUTRAL      2   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     25  119
  FC.LOW.NONSIG    5   35
  FC.NEUTRAL       2    8
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO           25             5          2
  YES         119            35          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"
D2V8, continuous
D2V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.SIG                                  6    14
  FC.LOW.NONSIG                                2     4
  FC.NEUTRAL                                   0     1
               vv
clus            BLACK OR AFRICAN AMERICAN
  FC.HIGH.SIG                           8
  FC.LOW.NONSIG                         5
  FC.NEUTRAL                            3
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FC.HIGH.SIG                                           1   106
  FC.LOW.NONSIG                                         0    27
  FC.NEUTRAL                                            0     5
D2V10, multiclass
                                           clus
vv                                          FC.HIGH.SIG FC.LOW.NONSIG
  AMERICAN INDIAN OR ALASKA NATIVE                    6             2
  ASIAN                                              14             4
  BLACK OR AFRICAN AMERICAN                           8             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             0
  WHITE                                             106            27
                                           clus
vv                                          FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE                   0
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0
  WHITE                                              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"
D2V11, binary
               cls
clus             0  1
  FC.HIGH.SIG    9 96
  FC.LOW.NONSIG  5 31
  FC.NEUTRAL     0  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      9   96
  FC.LOW.NONSIG    5   31
  FC.NEUTRAL       0    7
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               9             5          0
  NOT HISPANIC OR LATINO          96            31          7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
D2V13, binary
               cls
clus             0  1
  FC.HIGH.SIG   66 22
  FC.LOW.NONSIG 23  8
  FC.NEUTRAL     8  1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     66   22
  FC.LOW.NONSIG   23    8
  FC.NEUTRAL       8    1
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  TUMOR FREE          66            23          8
  WITH TUMOR          22             8          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            CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  FC.HIGH.SIG        4      7       3           118      12
  FC.LOW.NONSIG      0      3       2            34       1
  FC.NEUTRAL         1      0       1             7       1
D2V14, multiclass
               clus
vv              FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  CANADA                  4             0          1
  RUSSIA                  7             3          0
  UKRAINE                 3             2          1
  UNITED STATES         118            34          7
  VIETNAM                12             1          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            G1 G2 G3 G4 GX
  FC.HIGH.SIG   11 65 60  1  6
  FC.LOW.NONSIG  2 20 16  0  2
  FC.NEUTRAL     1  3  6  0  0
D2V15, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  G1          11             2          1
  G2          65            20          3
  G3          60            16          6
  G4           1             0          0
  GX           6             2          0
[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"
D2V16, continuous
[1] "Remove cluster labels:" "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           21             6             2 
   TCGA-BI-A0VR    TCGA-C5-A1BJ    TCGA-C5-A1BL    TCGA-C5-A1BQ    TCGA-C5-A1ME 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A1MF    TCGA-C5-A1MH    TCGA-C5-A2M2    TCGA-C5-A3HD    TCGA-C5-A7CM 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A7CO    TCGA-DG-A2KK    TCGA-DS-A3LQ    TCGA-EK-A2RA    TCGA-EX-A69M 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-FU-A2QG    TCGA-FU-A3TX    TCGA-FU-A3WB    TCGA-HM-A4S6    TCGA-IR-A3LB 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-IR-A3LH    TCGA-JX-A3Q0    TCGA-MU-A5YI    TCGA-Q1-A6DW    TCGA-Q1-A73S 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-RA-A741    TCGA-WL-A834 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" 
D2V17, continuous
               vv
clus            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  FC.HIGH.SIG                                            19
  FC.LOW.NONSIG                                           5
  FC.NEUTRAL                                              2
               vv
clus            CURRENT REFORMED SMOKER FOR > 15 YEARS
  FC.HIGH.SIG                                        6
  FC.LOW.NONSIG                                      2
  FC.NEUTRAL                                         0
               vv
clus            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  FC.HIGH.SIG                                                 1             27
  FC.LOW.NONSIG                                               0              7
  FC.NEUTRAL                                                  0              3
               vv
clus            LIFELONG NON-SMOKER
  FC.HIGH.SIG                    70
  FC.LOW.NONSIG                  20
  FC.NEUTRAL                      3
D2V18, multiclass
                                                 clus
vv                                                FC.HIGH.SIG FC.LOW.NONSIG
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS              19             5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                    6             2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED           1             0
  CURRENT SMOKER                                           27             7
  LIFELONG NON-SMOKER                                      70            20
                                                 clus
vv                                                FC.NEUTRAL
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS              2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                   0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED          0
  CURRENT SMOKER                                           3
  LIFELONG NON-SMOKER                                      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"
D2V19, continuous
D2V20, continuous
               vv
clus            COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  FC.HIGH.SIG            18       40             8        0        5
  FC.LOW.NONSIG           2       11             2        1        1
  FC.NEUTRAL              0        3             2        0        1
D2V21, multiclass
               clus
vv              FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  COMBINATION            18             2          0
  EXTERNAL               40            11          3
  EXTERNAL BEAM           8             2          2
  IMPLANTS                0             1          0
  INTERNAL                5             1          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"
D2V22, binary
               cls
clus             0  1
  FC.HIGH.SIG   21  3
  FC.LOW.NONSIG  4  0
  FC.NEUTRAL     1  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     21    3
  FC.LOW.NONSIG    4    0
  FC.NEUTRAL       1    0
                         clus
vv                        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  COMPLETED AS PLANNED             21             4          1
  TREATMENT NOT COMPLETED           3             0          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
  FC.HIGH.SIG                    1                1                  15
  FC.LOW.NONSIG                  1                1                   4
  FC.NEUTRAL                     0                0                   1
               vv
clus            REGIONAL SITE
  FC.HIGH.SIG               3
  FC.LOW.NONSIG             0
  FC.NEUTRAL                1
D2V23, multiclass
[1] "Remove cluster labels:" "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           20             6             2 
   TCGA-C5-A0TN    TCGA-C5-A1BF    TCGA-C5-A1BQ    TCGA-C5-A2LZ    TCGA-C5-A7CK 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-C5-A7CL    TCGA-C5-A7CM    TCGA-C5-A7CO    TCGA-C5-A7UH    TCGA-C5-A7X3 
  "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-DG-A2KL    TCGA-DS-A7WF    TCGA-EA-A43B    TCGA-EX-A3L1    TCGA-FU-A23L 
  "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-FU-A3HY    TCGA-FU-A3HZ    TCGA-HM-A3JJ    TCGA-HM-A4S6    TCGA-IR-A3LF 
  "FC.HIGH.SIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-IR-A3LH    TCGA-JW-A5VG    TCGA-JX-A3Q0    TCGA-JX-A5QV    TCGA-R2-A69V 
  "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" 
   TCGA-WL-A834 
  "FC.HIGH.SIG" 
                     clus
vv                    FC.HIGH.SIG FC.LOW.NONSIG
  DISTANT RECURRENCE            1             1
  LOCAL RECURRENCE              1             1
  PRIMARY TUMOR FIELD          15             4
  REGIONAL SITE                 3             0
[1] 4 2
[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
  FC.HIGH.SIG   10  3
  FC.LOW.NONSIG  6  0
  FC.NEUTRAL     0  1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     10    3
  FC.LOW.NONSIG    6    0
  FC.NEUTRAL       0    1
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  CGY          10             6          0
  GY            3             0          1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, continuous
               vv
clus            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FC.HIGH.SIG                                     1
  FC.LOW.NONSIG                                   1
  FC.NEUTRAL                                      0
               vv
clus            MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FC.HIGH.SIG                                     6                      21
  FC.LOW.NONSIG                                   1                       5
  FC.NEUTRAL                                      0                       2
               vv
clus            POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FC.HIGH.SIG                         1                       5
  FC.LOW.NONSIG                       0                       1
  FC.NEUTRAL                          0                       0
D2V31, multiclass
[1] "Remove cluster labels:" "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           34             8             2 
   TCGA-BI-A20A    TCGA-C5-A0TN    TCGA-C5-A1BE    TCGA-C5-A1BK    TCGA-C5-A1BM 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-C5-A1M5    TCGA-C5-A1M7    TCGA-C5-A1M8    TCGA-C5-A1M9    TCGA-C5-A1ME 
"FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A1MF    TCGA-C5-A1MJ    TCGA-C5-A1MP    TCGA-C5-A1MQ    TCGA-C5-A2LS 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-C5-A2LX    TCGA-C5-A2M1    TCGA-C5-A3HE    TCGA-C5-A3HL    TCGA-C5-A7CG 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A7CJ    TCGA-C5-A7UC    TCGA-DG-A2KL    TCGA-DR-A0ZM    TCGA-DS-A0VK 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-DS-A0VL    TCGA-DS-A0VM    TCGA-DS-A0VN    TCGA-DS-A1OA    TCGA-DS-A3LQ 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EA-A50E    TCGA-EK-A2RN    TCGA-EK-A2RO    TCGA-EX-A1H5    TCGA-EX-A449 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-FU-A3EO    TCGA-HM-A4S6    TCGA-IR-A3LH    TCGA-IR-A3LI    TCGA-IR-A3LK 
"FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-UC-A7PD    TCGA-WL-A834 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" 
                                     clus
vv                                    FC.HIGH.SIG FC.LOW.NONSIG
  MACROSCOPIC PARAMETRIAL INVOLVEMENT           1             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT           6             1
  OTHER LOCATION, SPECIFY                      21             5
  POSITIVE BLADDER MARGIN                       1             0
  POSITIVE VAGINAL MARGIN                       5             1
[1] 5 2
[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)
  FC.HIGH.SIG                                               1
  FC.LOW.NONSIG                                             1
  FC.NEUTRAL                                                0
               vv
clus            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  FC.HIGH.SIG                                                9
  FC.LOW.NONSIG                                              0
  FC.NEUTRAL                                                 1
               vv
clus            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  FC.HIGH.SIG                                                                                  48
  FC.LOW.NONSIG                                                                                 8
  FC.NEUTRAL                                                                                    4
               vv
clus            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  FC.HIGH.SIG                                                                                             59
  FC.LOW.NONSIG                                                                                           26
  FC.NEUTRAL                                                                                               3
D2V32, multiclass
                                                                                              clus
vv                                                                                             FC.HIGH.SIG
  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)                     48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)          59
                                                                                              clus
vv                                                                                             FC.LOW.NONSIG
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  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)            26
                                                                                              clus
vv                                                                                             FC.NEUTRAL
  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)                     4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)          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"
D2V33, binary
               cls
clus             0  1
  FC.HIGH.SIG   44 51
  FC.LOW.NONSIG 14 15
  FC.NEUTRAL     5  1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     44   51
  FC.LOW.NONSIG   14   15
  FC.NEUTRAL       5    1
         clus
vv        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ABSENT           44            14          5
  PRESENT          51            15          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"
D2V34, continuous
D2V35, continuous
D2V36, binary
               cls
clus             0  1
  FC.HIGH.SIG   33 61
  FC.LOW.NONSIG  4 21
  FC.NEUTRAL     2  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     33   61
  FC.LOW.NONSIG    4   21
  FC.NEUTRAL       2    4
                                          clus
vv                                         FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  KERATINIZING SQUAMOUS CELL CARCINOMA              33             4          2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA          61            21          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"
D2V37, continuous
               vv
clus            CURRENT USER FORMER USER NEVER USED
  FC.HIGH.SIG              5          32         29
  FC.LOW.NONSIG            2          10         15
  FC.NEUTRAL               1           1          2
D2V38, multiclass
              clus
vv             FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  CURRENT USER           5             2          1
  FORMER USER           32            10          1
  NEVER USED            29            15          2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V39, continuous
D2V40, binary
               cls
clus             0  1
  FC.HIGH.SIG   63 11
  FC.LOW.NONSIG 20  5
  FC.NEUTRAL     5  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     63   11
  FC.LOW.NONSIG   20    5
  FC.NEUTRAL       5    0
         clus
vv        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ABSENT           63            20          5
  PRESENT          11             5          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
  FC.HIGH.SIG             1        12     1
  FC.LOW.NONSIG           1         3     0
  FC.NEUTRAL              0         1     0
D2V41, multiclass
[1] "Remove cluster labels:" "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           14             4             1 
   TCGA-C5-A1BE    TCGA-C5-A1BI    TCGA-C5-A1BN    TCGA-C5-A1M9    TCGA-C5-A1MH 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-C5-A1MI    TCGA-C5-A1MK    TCGA-C5-A1MN    TCGA-C5-A1MQ    TCGA-C5-A2LX 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-C5-A2LY    TCGA-C5-A3HD    TCGA-DR-A0ZM    TCGA-DS-A1OA    TCGA-DS-A3LQ 
"FC.LOW.NONSIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EK-A2H0    TCGA-EK-A2H1    TCGA-HM-A3JJ 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
             clus
vv            FC.HIGH.SIG FC.LOW.NONSIG
  CARBOPLATIN           1             1
  CISPLATIN            12             3
  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:" "FC.LOW.NONSIG"          "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            8             1             1 
 TCGA-C5-A1BN  TCGA-C5-A1MH  TCGA-C5-A1ML  TCGA-C5-A1MN  TCGA-C5-A1MP 
"FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" 
 TCGA-EK-A2RO  TCGA-JW-A852  TCGA-MU-A51Y 
"FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" 
               vv
clus            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  FC.HIGH.SIG      1  14   43   14  4   5    6    6   9  1   1  1  8
  FC.LOW.NONSIG    0   3   14    8  0   2    0    4   3  0   1  1  1
  FC.NEUTRAL       0   4    3    0  0   0    0    0   1  0   0  0  0
D2V43, multiclass
      clus
vv     FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1A1           1             0          0
  T1B           14             3          4
  T1B1          43            14          3
  T1B2          14             8          0
  T2             4             0          0
  T2A            5             2          0
  T2A1           6             0          0
  T2A2           6             4          0
  T2B            9             3          1
  T3             1             0          0
  T3B            1             1          0
  T4             1             1          0
  TX             8             1          0
[1] 13  3
[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
  FC.HIGH.SIG         3        0         1         1       21        37
  FC.LOW.NONSIG       1        0         0         0        5        12
  FC.NEUTRAL          0        1         0         0        2         4
               vv
clus            STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  FC.HIGH.SIG          19        4         4          5          3        12
  FC.LOW.NONSIG        10        0         2          0          3         2
  FC.NEUTRAL            0        0         0          0          1         0
               vv
clus            STAGE III STAGE IIIB STAGE IVA STAGE IVB
  FC.HIGH.SIG           1         25         2         2
  FC.LOW.NONSIG         0          2         0         3
  FC.NEUTRAL            0          2         0         0
D2V45, multiclass
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I              3             1          0
  STAGE IA             0             0          1
  STAGE IA1            1             0          0
  STAGE IA2            1             0          0
  STAGE IB            21             5          2
  STAGE IB1           37            12          4
  STAGE IB2           19            10          0
  STAGE II             4             0          0
  STAGE IIA            4             2          0
  STAGE IIA1           5             0          0
  STAGE IIA2           3             3          1
  STAGE IIB           12             2          0
  STAGE III            1             0          0
  STAGE IIIB          25             2          2
  STAGE IVA            2             0          0
  STAGE IVB            2             3          0
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
