[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/19775059/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/20124378/CESC-TP.mergedcluster.txt"

nPatients in clinical file=307, in cluster file=307, common to both=307
[1]  10 307
[1] "CN_CNMF"
[1] 3
  1   2   3 
129  73  93 
  1   2   3 
129  73  93 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6 
71 58 60 61 11 46 
 1  2  3  4  5  6 
71 58 60 61 11 46 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6  7  8 
26 26 20 21 33 27  7 13 
 1  2  3  4  5  6  7  8 
26 26 20 21 33 27  7 13 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
32 49 51 23 18 
 1  2  3  4  5 
32 49 51 23 18 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
 58 105  69  72 
  1   2   3   4 
 58 105  69  72 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 72 195  37 
  1   2   3 
 72 195  37 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
103  80 124 
  1   2   3 
103  80 124 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 60 102  74  26  45 
  1   2   3   4   5 
 60 102  74  26  45 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
129  78  87 
  1   2   3 
129  78  87 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 64  50  31 149 
  1   2   3   4 
 64  50  31 149 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                          
 [2] "VITAL_STATUS"                            
 [3] "DAYS_TO_DEATH"                           
 [4] "DAYS_TO_LAST_FOLLOWUP"                   
 [5] "TUMOR_TISSUE_SITE"                       
 [6] "PATHOLOGIC_STAGE"                        
 [7] "PATHOLOGY_T_STAGE"                       
 [8] "PATHOLOGY_N_STAGE"                       
 [9] "PATHOLOGY_M_STAGE"                       
[10] "GENDER"                                  
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"    
[12] "RADIATION_THERAPY"                       
[13] "HISTOLOGICAL_TYPE"                       
[14] "NUMBER_PACK_YEARS_SMOKED"                
[15] "NUMBER_OF_LYMPH_NODES"                   
[16] "RACE"                                    
[17] "ETHNICITY"                               
[18] "WEIGHT_KG_AT_DIAGNOSIS"                  
[19] "TUMOR_STATUS"                            
[20] "NEOPLASM_HISTOLOGIC_GRADE"               
[21] "TOBACCO_SMOKING_YEAR_STOPPED"            
[22] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"       
[23] "TOBACCO_SMOKING_HISTORY"                 
[24] "AGEBEGANSMOKINGINYEARS"                  
[25] "RADIATION_THERAPY_STATUS"                
[26] "PREGNANCIES_COUNT_TOTAL"                 
[27] "PREGNANCIES_COUNT_STILLBIRTH"            
[28] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"    
[29] "PREGNANCIES_COUNT_LIVE_BIRTH"            
[30] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"    
[31] "PREGNANCIES_COUNT_ECTOPIC"               
[32] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT"
[33] "LYMPH_NODE_LOCATION"                     
[34] "POS_LYMPH_NODE_LOCATION"                 
[35] "MENOPAUSE_STATUS"                        
[36] "LYMPHOVASCULAR_INVOLVEMENT"              
[37] "LYMPH_NODES_EXAMINED_HE_COUNT"           
[38] "LYMPH_NODES_EXAMINED"                    
[39] "KERATINIZATION_SQUAMOUS_CELL"            
[40] "INITIAL_PATHOLOGIC_DX_YEAR"              
[41] "HYSTERECTOMY_TYPE"                       
[42] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"     
[43] "HEIGHT_CM_AT_DIAGNOSIS"                  
[44] "CORPUS_INVOLVEMENT"                      
[45] "CHEMO_CONCURRENT_TYPE"                   
[46] "CERVIX_SUV_RESULTS"                      
[47] "CAUSE_OF_DEATH"                          
[48] "AGE_AT_DIAGNOSIS"                        
[49] "CLINICAL_STAGE"                          

Input Data has 49 rows and 307 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=213,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'PREGNANCY_SPONTANEOUS_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 29:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'PREGNANCY_THERAPEUTIC_ABORTION_COUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 31:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 32:'CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              BILATERAL PELVIC WALL INVOLVEMENT ON IMAGING
freq.values   "1"                                         
freq.contrast "10"                                        
both >= 3     "FALSE"                                     
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "10"                                                                                                                               
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NEGATIVE NO EXTENSION NO PELVIC SPREAD
freq.values   "1"                       "2"      "1"          "1"             
freq.contrast "10"                      "9"      "10"         "10"            
both >= 3     "FALSE"                   "FALSE"  "FALSE"      "FALSE"         
              PELVIC SPREAD
freq.values   "1"          
freq.contrast "10"         
both >= 3     "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "10"                                                                        
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "10"                                                                                                                                      
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "10"                                                                     
both >= 3     "FALSE"                                                                  
Variable 33:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 34:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 35:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 36:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 37:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 40:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 41:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'CAUSE_OF_DEATH':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARDIOPULMONARY ARREST LUNG CANCER RENAL FAILURE
freq.values   "1"                    "1"         "1"          
freq.contrast "2"                    "2"         "2"          
both >= 3     "FALSE"                "FALSE"     "FALSE"      
Variable 48:'AGE_AT_DIAGNOSIS':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'CLINICAL_STAGE':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 307 columns, 1 survival variables, and 38 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                      
 [2] "PATHOLOGY_T_STAGE"                   
 [3] "PATHOLOGY_N_STAGE"                   
 [4] "PATHOLOGY_M_STAGE"                   
 [5] "RADIATION_THERAPY"                   
 [6] "HISTOLOGICAL_TYPE"                   
 [7] "NUMBER_PACK_YEARS_SMOKED"            
 [8] "NUMBER_OF_LYMPH_NODES"               
 [9] "RACE"                                
[10] "ETHNICITY"                           
[11] "WEIGHT_KG_AT_DIAGNOSIS"              
[12] "TUMOR_STATUS"                        
[13] "NEOPLASM_HISTOLOGIC_GRADE"           
[14] "TOBACCO_SMOKING_YEAR_STOPPED"        
[15] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"   
[16] "TOBACCO_SMOKING_HISTORY"             
[17] "AGEBEGANSMOKINGINYEARS"              
[18] "RADIATION_THERAPY_STATUS"            
[19] "PREGNANCIES_COUNT_TOTAL"             
[20] "PREGNANCIES_COUNT_STILLBIRTH"        
[21] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"
[22] "PREGNANCIES_COUNT_LIVE_BIRTH"        
[23] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"
[24] "PREGNANCIES_COUNT_ECTOPIC"           
[25] "POS_LYMPH_NODE_LOCATION"             
[26] "MENOPAUSE_STATUS"                    
[27] "LYMPHOVASCULAR_INVOLVEMENT"          
[28] "LYMPH_NODES_EXAMINED_HE_COUNT"       
[29] "LYMPH_NODES_EXAMINED"                
[30] "KERATINIZATION_SQUAMOUS_CELL"        
[31] "INITIAL_PATHOLOGIC_DX_YEAR"          
[32] "HISTORY_HORMONAL_CONTRACEPTIVES_USE" 
[33] "HEIGHT_CM_AT_DIAGNOSIS"              
[34] "CORPUS_INVOLVEMENT"                  
[35] "CHEMO_CONCURRENT_TYPE"               
[36] "CERVIX_SUV_RESULTS"                  
[37] "AGE_AT_DIAGNOSIS"                    
[38] "CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
141  72  21  10 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
141  72  21  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
141  72  21  10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


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

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 99 25
  subtype2 45 21
  subtype3 67 21
subtype1 subtype2 subtype3 
     124       66       88 
subtype1 subtype2 subtype3 
      25       21       21 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM 
       17.52        18.74        36.56       144.16       177.04        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       19.86        46.32        35.01        38.99         0.46         2.43 
TCGA-C5-A1MP TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        3.58        38.43        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XJ TCGA-C5-A8YT 
      101.82        17.19        94.95         9.34       146.86        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN 
       20.91         1.12        44.94        63.98        58.88        95.67 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       16.83        16.18        39.55        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A6QX 
       26.40         0.30        24.82         7.46        26.79        24.00 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R8 TCGA-EK-A2RC TCGA-EK-A3GJ TCGA-EK-A3GK 
       26.27         6.64         1.45         4.31         0.10         0.49 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
        7.92        15.22        14.70        15.55         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JK 
       28.31        35.44         1.12        17.75        25.41        20.78 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LL 
        9.44       147.39       137.16        66.81        96.95        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MA-AA3Y 
      209.59        44.61        11.28        12.49         0.30        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35         8.52        28.08        34.62        19.96 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
       35.05        20.84        15.58        16.14        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EL 
       18.64        19.59        14.60        11.67        69.50        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 
       53.59        39.78        31.27        33.37        58.45        50.14 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UR 
       48.39        28.50        29.95        46.92         1.71        26.07 
TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       14.53        67.20         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZX-AA5X 
       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 
       17.82        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        14.73 
TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A411 TCGA-EA-A439 
       95.11        69.96        17.52         8.28        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2H0 TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       26.01        14.89        60.72         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GM TCGA-FU-A23L 
        0.36        40.96         0.43         0.53         0.76        23.84 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK 
       14.01        10.55        16.57        21.67        78.71        29.85 
TCGA-JX-A3PZ TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73S 
       21.11        11.38        17.23         2.96         9.04        22.62 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94X 
       12.16        10.03        23.97        19.96        59.18        16.64 
TCGA-VS-A94Y TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UL 
        4.73        51.32        50.47        27.12        45.11        14.53 
TCGA-VS-A9UT TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       15.85        18.25        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        82.06        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       36.76        55.63        22.98        40.87        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        25.91        27.29        27.25        27.22 
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-A3GN TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M 
        0.10        47.77         0.03        20.35        19.79         8.32 
TCGA-FU-A3NI TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LI TCGA-JW-A5VK TCGA-JW-A852 
       20.98        14.93       129.37        81.96        20.48         8.28 
TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       18.15        20.91         0.89         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73Q 
       19.56        54.81        16.41        15.95        17.56         9.34 
TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QA 
       93.99        46.52        45.57        32.42        32.15        36.13 
TCGA-VS-A8QC TCGA-VS-A94W TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       11.51        40.87        40.14        15.68        56.35        55.50 
TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
       43.40        24.30        27.25        47.87        47.47        41.52 
TCGA-VS-A9UV TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        3.42        26.01         1.41         0.16 

subtype1 subtype2 subtype3 
    0.10     0.36     0.03 
subtype1 subtype2 subtype3 
  210.67   147.35   173.29 
subtype1 subtype2 subtype3 
  20.795   20.730   27.270 
[1] "0.1 - 210.7 (20.8)" "0.4 - 147.3 (20.7)" "0.0 - 173.3 (27.3)"
D1V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 61 37  5  4
  subtype2 30 18  6  1
  subtype3 44 15 10  3
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       61       30       44
  T2       37       18       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 67 21
  subtype2 25 17
  subtype3 37 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   21
  subtype2   25   17
  subtype3   37   18
   clus
vv  subtype1 subtype2 subtype3
  0       67       25       37
  1       21       17       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 44  5
  subtype2 23  3
  subtype3 41  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    5
  subtype2   23    3
  subtype3   41    2
   clus
vv  subtype1 subtype2 subtype3
  0       44       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"
D1V6, binary
          cls
clus        0  1
  subtype1 28 49
  subtype2  8 33
  subtype3 19 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   49
  subtype2    8   33
  subtype3   19   41
     clus
vv    subtype1 subtype2 subtype3
  NO        28        8       19
  YES       49       33       41
[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                               97
  subtype2             2                               61
  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                                   3
  subtype3                                   4
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         1
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            9
  subtype2                                            4
  subtype3                                            4
D1V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    97       61       84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        3        2        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        3        4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        1        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         9        4        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"
D1V8, continuous
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                6     7                        11
  subtype2                                0     2                         8
  subtype3                                2    10                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    91
  subtype2                                         1    54
  subtype3                                         0    57
D1V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 6        0        2
  ASIAN                                            7        2       10
  BLACK OR AFRICAN AMERICAN                       11        8        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        1        0
  WHITE                                           91       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 71
  subtype2  5 40
  subtype3  5 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   71
  subtype2    5   40
  subtype3    5   51
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        5        5
  NOT HISPANIC OR LATINO       71       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 88 27
  subtype2 37 23
  subtype3 58 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   88   27
  subtype2   37   23
  subtype3   58   24
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       88       37       58
  WITH TUMOR       27       23       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"
          vv
clus       G1 G2 G3 G4 GX
  subtype1 10 58 49  0 10
  subtype2  2 20 37  1  7
  subtype3  6 51 29  0  7
D1V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1       10        2        6
  G2       58       20       51
  G3       49       37       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"
D1V15, continuous
D1V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          16
  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                  28
  subtype3                  44
D1V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           16       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       28       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"
D1V18, continuous
D1V19, 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"
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                      17
  subtype2                                   3                       8
  subtype3                                   3                      11
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       4
  subtype2                       0                       1
  subtype3                       0                       3
D1V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        3
  OTHER LOCATION, SPECIFY                   17        8       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                                                                                17
  subtype3                                                                                32
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           63
  subtype2                                                                                           30
  subtype3                                                                                           28
D1V27, 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)       63
                                                                                              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)                  17
  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"
D1V28, binary
          cls
clus        0  1
  subtype1 39 33
  subtype2 10 19
  subtype3 22 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   33
  subtype2   10   19
  subtype3   22   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        39       10       22
  PRESENT       33       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"
D1V29, continuous
D1V30, continuous
D1V31, binary
          cls
clus        0  1
  subtype1 21 51
  subtype2 11 27
  subtype3 17 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   51
  subtype2   11   27
  subtype3   17   39
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           21       11       17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       51       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"
D1V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            9          28         33
  subtype2            3          12         20
  subtype3            3          14         32
D1V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        9        3        3
  FORMER USER        28       12       14
  NEVER USED         33       20       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"
D1V34, continuous
D1V35, binary
          cls
clus        0  1
  subtype1 46  7
  subtype2 15  5
  subtype3 31  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    7
  subtype2   15    5
  subtype3   31    6
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        46       15       31
  PRESENT        7        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           4        41     2
  subtype2           0        32     0
  subtype3           1        27     0
D1V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        4        0        1
  CISPLATIN         41       32       27
  OTHER              2        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"
D1V37, continuous
D1V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         1         0       12        40        17
  subtype2       2        0         0         1        9        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        17         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
D1V39, 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        9       13
  STAGE IB1        40       13       24
  STAGE IB2        17       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       17       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 53 16
  subtype2 42 13
  subtype3 46 11
  subtype4 34 21
  subtype5 10  1
  subtype6 34  9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      69       55       57       55       11       43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      16       13       11       21        1        9 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ 
       17.52        31.40        35.01        57.73        35.61         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-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH 
        2.73         1.12        95.11        82.06        16.18        17.52 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZF 
       26.40        24.56        31.73        24.82        14.89        27.22 
TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EX-A1H6 TCGA-EX-A449 
        0.36        47.77         0.49         0.76         7.92        14.70 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.22        16.11        36.26        14.01        35.44         1.12 
TCGA-HG-A9SC TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI 
       16.57         9.44       137.16        66.81        96.95        81.96 
TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BD 
        3.29        28.37        44.61        13.35        11.38        54.81 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S 
        2.96        15.58        16.14        15.88        18.64        22.62 
TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ 
       69.50        19.96        36.13        39.78        58.45         1.71 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ 
       14.53        47.87        47.47        41.52        26.07        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 
       18.84         5.16        16.24 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A7CO 
       17.82       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        69.96        28.90 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A6QX 
       40.87        37.35        13.05         0.30        26.79        24.00 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RA TCGA-EK-A2RC TCGA-FU-A2QG TCGA-FU-A3HY 
        6.64         1.51        40.96         4.31        19.04        31.36 
TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VK 
       26.14        10.55       147.39       129.37        29.85        20.48 
TCGA-JW-A5VL TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA41 
       15.58        18.15       209.59         0.82        19.56         8.35 
TCGA-MA-AA42 TCGA-Q1-A5R2 TCGA-UC-A7PG TCGA-VS-A8EK TCGA-VS-A8QC TCGA-VS-A8QF 
        8.52        16.41        12.16        27.25        11.51        59.18 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UI 
       40.14        15.68        56.35        50.47        48.39        45.11 
TCGA-VS-A9UM TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 
       27.25         3.42        18.25        18.25        17.75        26.01 
TCGA-ZJ-AAXA 
        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        63.98        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        27.29        13.48 
TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-EX-A69L 
       26.27         1.45         0.10         0.53        15.22        19.79 
TCGA-EX-A8YF TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AU 
       15.55        28.31        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        28.08        35.05        14.07 
TCGA-R2-A69V TCGA-VS-A8EI TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A958 
       19.59        23.97        31.27        40.87        33.37        50.14 
TCGA-VS-A959 TCGA-VS-A9UH TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-VS-AA62 
       51.32        46.92        15.85        14.53         4.34        15.42 
TCGA-XS-A8TJ TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26         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        14.73        95.67        12.36         8.28        36.89 
TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EK-A2H0 TCGA-EK-A2PK TCGA-EK-A2PL 
       26.01         7.46        25.91        60.72         0.39         0.43 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-GH-A9DA TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VI 
        0.10         0.03        17.75        78.71        27.42        24.56 
TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-Q1-A6DT TCGA-UC-A7PD 
       21.44        21.11        12.49        17.23         9.04        11.67 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A94X 
       10.03        32.42        65.49        32.15        53.59        16.64 
TCGA-VS-A94Y TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-ZJ-A8QQ 
        4.73        28.50        29.95        27.12        24.30        67.59 
TCGA-ZJ-A8QR 
       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-EK-A2RK TCGA-FU-A23L TCGA-Q1-A73Q TCGA-VS-A8EC 
        0.59         0.43        23.84         9.34        46.52 

$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        55.63 
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        27.25         0.36 
TCGA-EK-A2GZ TCGA-EK-A2PI TCGA-EK-A2R9 TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A3NI 
       12.59        19.27         0.13        20.35         8.32        20.98 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-HG-A2PA TCGA-HM-A3JK TCGA-JW-A852 TCGA-JX-A5QV 
        1.48        16.14        25.41        20.78         8.28        20.91 
TCGA-LP-A5U2 TCGA-MA-AA3Z TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R3 
        0.30        19.56        34.62        19.96        20.84        15.95 
TCGA-Q1-A6DW TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EG TCGA-VS-A957 TCGA-VS-A9U6 
       17.56        14.60        93.99        45.57        55.50        43.40 
TCGA-ZJ-AAX4 
        0.69 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.36     0.30     0.10     0.03     0.43     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  137.16   209.59   210.67   154.32   155.77   146.86 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   20.35    26.14    26.27    24.30    23.67    20.84 
[1] "0.4 - 137.2 (20.4)" "0.3 - 209.6 (26.1)" "0.1 - 210.7 (26.3)"
[4] "0.0 - 154.3 (24.3)" "0.4 - 155.8 (23.7)" "0.1 - 146.9 (20.8)"
D2V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 38 20  4  1
  subtype2 26 10  6  4
  subtype3 26 18  3  3
  subtype4 23 13  5  1
  subtype5  4  1  2  0
  subtype6 24 10  1  1
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       38       26       26       23        4       24
  T2       20       10       18       13        1       10
  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 38 12
  subtype2 19 14
  subtype3 25 16
  subtype4 25  8
  subtype5  4  2
  subtype6 24  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   12
  subtype2   19   14
  subtype3   25   16
  subtype4   25    8
  subtype5    4    2
  subtype6   24    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       38       19       25       25        4       24
  1       12       14       16        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 26  5
  subtype2 20  1
  subtype3 27  1
  subtype4 22  2
  subtype5  4  0
  subtype6 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    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       26       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"
D2V6, binary
          cls
clus        0  1
  subtype1 14 31
  subtype2 12 26
  subtype3  8 23
  subtype4 11 28
  subtype5  1  5
  subtype6 11 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   31
  subtype2   12   26
  subtype3    8   23
  subtype4   11   28
  subtype5    1    5
  subtype6   11   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        14       12        8       11        1       11
  YES       31       26       23       28        5       14
[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             6                               21
  subtype2             0                               58
  subtype3             0                               58
  subtype4             0                               61
  subtype5             0                               11
  subtype6             0                               45
          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                                  21
  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                                           15
  subtype2                                            0
  subtype3                                            2
  subtype4                                            0
  subtype5                                            0
  subtype6                                            0
D2V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        6        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    21       58       58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 21        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        15        0        2
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    61       11       45
  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"
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     7                         7
  subtype4                                4     3                         8
  subtype5                                0     0                         0
  subtype6                                1     2                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    53
  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        7        3
  BLACK OR AFRICAN AMERICAN                        3        7        7        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           53       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 39
  subtype2  5 29
  subtype3  4 34
  subtype4  5 35
  subtype5  0  5
  subtype6  3 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   39
  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       39       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 43 20
  subtype2 37 14
  subtype3 43 11
  subtype4 32 20
  subtype5  7  3
  subtype6 29 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   20
  subtype2   37   14
  subtype3   43   11
  subtype4   32   20
  subtype5    7    3
  subtype6   29   10
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  TUMOR FREE       43       37       43       32        7       29
  WITH TUMOR       20       14       11       20        3       10
[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       G1 G2 G3 G4 GX
  subtype1  7 30 28  0  6
  subtype2  2 27 25  0  3
  subtype3  3 29 23  0  4
  subtype4  1 26 24  1  5
  subtype5  0  4  6  0  1
  subtype6  5 20 14  0  5
D2V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  G1        7        2        3        1        0        5
  G2       30       27       29       26        4       20
  G3       28       25       23       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"
D2V15, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9        9        7        7        1       10 
 [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [7] "subtype6" "subtype3" "subtype1" "subtype4" "subtype1" "subtype2"
[13] "subtype4" "subtype4" "subtype1" "subtype2" "subtype6" "subtype2"
[19] "subtype6" "subtype6" "subtype6" "subtype3" "subtype2" "subtype1"
[25] "subtype4" "subtype2" "subtype1" "subtype6" "subtype6" "subtype6"
[31] "subtype1" "subtype6" "subtype2" "subtype3" "subtype1" "subtype3"
[37] "subtype2" "subtype4" "subtype6" "subtype2" "subtype4" "subtype4"
D2V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           9
  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                  30
  subtype4                  26
  subtype5                   1
  subtype6                  18
D2V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            9        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       30
                                                 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"
D2V18, continuous
D2V19, 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"
D2V20, continuous
D2V21, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      27       23       20       22        2       18 
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype6" "subtype3"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype4" "subtype3"
 [13] "subtype2" "subtype1" "subtype3" "subtype6" "subtype1" "subtype1"
 [19] "subtype6" "subtype3" "subtype1" "subtype1" "subtype3" "subtype6"
 [25] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [31] "subtype2" "subtype4" "subtype2" "subtype1" "subtype1" "subtype4"
 [37] "subtype1" "subtype1" "subtype6" "subtype3" "subtype4" "subtype3"
 [43] "subtype6" "subtype4" "subtype2" "subtype2" "subtype4" "subtype1"
 [49] "subtype6" "subtype3" "subtype6" "subtype6" "subtype2" "subtype4"
 [55] "subtype3" "subtype2" "subtype4" "subtype3" "subtype6" "subtype1"
 [61] "subtype1" "subtype4" "subtype3" "subtype2" "subtype2" "subtype6"
 [67] "subtype6" "subtype3" "subtype2" "subtype3" "subtype4" "subtype1"
 [73] "subtype1" "subtype2" "subtype1" "subtype4" "subtype1" "subtype2"
 [79] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype6"
 [85] "subtype6" "subtype2" "subtype2" "subtype1" "subtype4" "subtype1"
 [91] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [97] "subtype2" "subtype2" "subtype1" "subtype6" "subtype4" "subtype2"
[103] "subtype1" "subtype6" "subtype6" "subtype4" "subtype6" "subtype2"
[109] "subtype1" "subtype3"
D2V22, continuous
D2V23, continuous
D2V24, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      29       24       22       24        2       21 
  [1] "subtype1" "subtype2" "subtype4" "subtype4" "subtype6" "subtype3"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype4" "subtype3"
 [13] "subtype2" "subtype1" "subtype3" "subtype6" "subtype1" "subtype1"
 [19] "subtype6" "subtype3" "subtype1" "subtype1" "subtype3" "subtype6"
 [25] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [31] "subtype2" "subtype4" "subtype2" "subtype1" "subtype1" "subtype4"
 [37] "subtype1" "subtype1" "subtype6" "subtype3" "subtype4" "subtype3"
 [43] "subtype6" "subtype4" "subtype2" "subtype2" "subtype4" "subtype1"
 [49] "subtype6" "subtype3" "subtype6" "subtype6" "subtype2" "subtype4"
 [55] "subtype3" "subtype2" "subtype4" "subtype3" "subtype6" "subtype1"
 [61] "subtype1" "subtype4" "subtype3" "subtype2" "subtype2" "subtype6"
 [67] "subtype6" "subtype6" "subtype3" "subtype2" "subtype3" "subtype4"
 [73] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype4"
 [79] "subtype2" "subtype6" "subtype3" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype6"
 [91] "subtype3" "subtype6" "subtype2" "subtype2" "subtype1" "subtype4"
 [97] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype4"
[103] "subtype4" "subtype2" "subtype2" "subtype1" "subtype6" "subtype4"
[109] "subtype2" "subtype1" "subtype6" "subtype6" "subtype3" "subtype4"
[115] "subtype6" "subtype4" "subtype6" "subtype2" "subtype1" "subtype3"
D2V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       8
  subtype2                                   2                       4
  subtype3                                   0                      13
  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
D2V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        0        2
  OTHER LOCATION, SPECIFY                    8        4       13        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                                                                                18
  subtype4                                                                                 8
  subtype5                                                                                 3
  subtype6                                                                                18
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           35
  subtype2                                                                                           17
  subtype3                                                                                           27
  subtype4                                                                                           27
  subtype5                                                                                            4
  subtype6                                                                                           15
D2V27, 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)       35
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  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)                  18
  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"
D2V28, binary
          cls
clus        0  1
  subtype1 22 21
  subtype2  7 17
  subtype3 17 14
  subtype4 12  9
  subtype5  2  4
  subtype6 12 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   21
  subtype2    7   17
  subtype3   17   14
  subtype4   12    9
  subtype5    2    4
  subtype6   12   15
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        22        7       17       12        2       12
  PRESENT       21       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"
D2V29, continuous
D2V30, continuous
D2V31, binary
          cls
clus        0  1
  subtype1  0 17
  subtype2  6 31
  subtype3 13 26
  subtype4 18 22
  subtype5  5  3
  subtype6 13 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   17
  subtype2    6   31
  subtype3   13   26
  subtype4   18   22
  subtype5    5    3
  subtype6   13   21
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0        6       13       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17       31       26       22
                                          clus
vv                                         subtype5 subtype6
  KERATINIZING SQUAMOUS CELL CARCINOMA            5       13
  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"
D2V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          19         20
  subtype2            2          11         18
  subtype3            3           7         18
  subtype4            2          10         17
  subtype5            0           2          1
  subtype6            1           5         16
D2V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CURRENT USER        7        2        3        2        0        1
  FORMER USER        19       11        7       10        2        5
  NEVER USED         20       18       18       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"
D2V34, continuous
D2V35, binary
          cls
clus        0  1
  subtype1 31  6
  subtype2 15  2
  subtype3 18  5
  subtype4 15  1
  subtype5  2  2
  subtype6 18  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    6
  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        6        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           3        23     1
  subtype2           1        20     0
  subtype3           1        22     1
  subtype4           1        26     0
  subtype5           1         3     0
  subtype6           0        10     0
D2V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CARBOPLATIN        3        1        1        1        1        0
  CISPLATIN         23       20       22       26        3       10
  OTHER              1        0        1        0        0        0
[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"
D2V37, 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"
D2V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        26        11
  subtype2       0        0         0         0        6        13         6
  subtype3       0        1         0         0        8        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         5         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
D2V39, 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        8       13        1        5
  STAGE IB1        26       13       18        9        2       10
  STAGE IB2        11        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        5
  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 20  6
  subtype2 15  9
  subtype3 14  3
  subtype4 20  1
  subtype5 25  6
  subtype6 22  3
  subtype7  6  1
  subtype8  9  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      26       24       17       21       31       25        7       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       6        9        3        1        6        3        1        1 
$subtype1
TCGA-2W-A8YY TCGA-C5-A0TN TCGA-C5-A1MH TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7X3 
       17.52        11.44        38.99        18.02        20.42         9.34 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A5FO TCGA-EK-A2H1 
       17.52        39.55        31.36        25.02        26.79        26.27 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A40J 
        0.59         1.45        14.70        19.79         8.32        14.01 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-LP-A4AW TCGA-MU-A5YI TCGA-Q1-A73O TCGA-Q1-A73Q 
       16.57        21.67         0.89        34.62        14.07         9.34 
TCGA-R2-A69V TCGA-ZJ-A8QR 
       19.59        19.13 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       17.82        31.40        35.01        40.93        73.18        73.45 
TCGA-C5-A8XI TCGA-C5-A907 TCGA-DS-A1OB TCGA-DS-A7WI TCGA-EA-A50E TCGA-EK-A2H0 
        8.35        14.73        28.31         8.28         7.46        60.72 
TCGA-EK-A2IP TCGA-EK-A2IR TCGA-FU-A2QG TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JX-A3PZ 
        6.64       113.16        19.04        78.71        29.85        21.11 
TCGA-MA-AA3Y TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BF TCGA-VS-A94X TCGA-WL-A834 
       17.82        11.38        19.96        20.84        16.64        26.01 

$subtype3
TCGA-C5-A1BJ TCGA-C5-A1M7 TCGA-C5-A1MP TCGA-C5-A3HF TCGA-DG-A2KH TCGA-DS-A0VK 
      144.16        46.32         3.58        17.85         1.12        36.76 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A5ZD TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GN 
       24.56        26.01        27.29        47.77         0.49         0.03 
TCGA-IR-A3LC TCGA-Q1-A5R3 TCGA-Q1-A73P TCGA-RA-A741 TCGA-VS-A8QF 
      129.37        15.95        15.88        14.60        59.18 

$subtype4
TCGA-C5-A1BL TCGA-C5-A2LY TCGA-C5-A7CG TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VM 
      173.29        78.35       210.67        82.06        63.98        69.96 
TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A3HU TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2RK 
       12.36       127.36        33.30         0.39         0.36         0.43 
TCGA-EX-A8YF TCGA-IR-A3LL TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA41 
       15.55        36.36        20.91        13.35        22.52         8.35 
TCGA-UC-A7PF TCGA-VS-A9U5 TCGA-VS-A9UB 
       93.99        50.47        29.95 

$subtype5
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MQ 
       67.46        57.73        53.16        35.61         0.46        33.90 
TCGA-C5-A2LX TCGA-C5-A2M2 TCGA-DS-A1O9 TCGA-DS-A3LQ TCGA-EA-A3QD TCGA-EA-A3Y4 
       83.05        33.24         8.75        22.98        13.05        36.89 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.40        31.73        24.82        14.89        27.22        24.00 
TCGA-EK-A2R9 TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A3TX TCGA-FU-A57G TCGA-IR-A3LA 
        0.13        20.35         1.22         1.48        35.44       137.16 
TCGA-IR-A3LB TCGA-IR-A3LI TCGA-LP-A5U2 TCGA-Q1-A73R TCGA-Q1-A73S TCGA-VS-A9UQ 
       66.81        81.96         0.30        18.64        22.62        41.52 
TCGA-VS-A9V0 
       18.84 

$subtype6
TCGA-C5-A1M8 TCGA-C5-A2LZ TCGA-C5-A7CK TCGA-DG-A2KL TCGA-DS-A0VN TCGA-DS-A1OA 
       30.21       100.14       134.33        44.94        95.67        28.90 
TCGA-DS-A5RQ TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A44S TCGA-EA-A5O9 TCGA-EA-A5ZE 
       16.83        37.35        31.53         0.30        25.91        27.25 
TCGA-EA-A78R TCGA-EK-A2PL TCGA-EK-A2RC TCGA-FU-A23L TCGA-FU-A3TQ TCGA-HM-A4S6 
       13.48         0.43         4.31        23.84        26.14        14.93 
TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U3 TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y 
       15.58       209.59         0.82        19.56         8.52        28.08 
TCGA-ZJ-AAXA 
        1.41 

$subtype7
TCGA-C5-A8XJ TCGA-DS-A0VL TCGA-EA-A1QT TCGA-LP-A4AX TCGA-MY-A913 TCGA-VS-A8EK 
      146.86        55.63        40.87        12.49        17.23        27.25 
TCGA-VS-A9UD 
       24.30 

$subtype8
TCGA-EA-A3HR TCGA-EA-A97N TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A3GM TCGA-GH-A9DA 
       30.90         0.36        40.96         0.10         0.76        17.75 
TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-Q1-A6DW 
       25.41       147.39        96.95        17.56 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.59     6.64     0.03     0.36     0.13     0.30    12.49     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   39.55   113.16   144.16   210.67   137.16   209.59   146.86   147.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  17.770   20.975   24.560   33.300   26.400   25.910   27.250   21.580 
[1] "0.6 - 39.5 (17.8)"   "6.6 - 113.2 (21.0)"  "0.0 - 144.2 (24.6)" 
[4] "0.4 - 210.7 (33.3)"  "0.1 - 137.2 (26.4)"  "0.3 - 209.6 (25.9)" 
[7] "12.5 - 146.9 (27.2)" "0.1 - 147.4 (21.6)" 
D3V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 16  3  0  0
  subtype2 14  4  2  1
  subtype3 12  1  1  0
  subtype4 13  6  0  0
  subtype5 21  7  1  1
  subtype6 13  8  1  0
  subtype7  3  0  1  1
  subtype8  7  3  1  0
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1       16       14       12       13       21       13        3        7
  T2        3        4        1        6        7        8        0        3
  T3        0        2        1        0        1        1        1        1
  T4        0        1        0        0        1        0        1        0
[1] 4 8
[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 13  4
  subtype2 13  6
  subtype3  9  5
  subtype4 10  8
  subtype5 18 10
  subtype6 15  5
  subtype7  4  0
  subtype8 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    4
  subtype2   13    6
  subtype3    9    5
  subtype4   10    8
  subtype5   18   10
  subtype6   15    5
  subtype7    4    0
  subtype8   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       13       13        9       10       18       15        4       11
  1        4        6        5        8       10        5        0        0
[1] 2 8
[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 10  1
  subtype2  9  0
  subtype3  8  0
  subtype4 14  1
  subtype5 18  1
  subtype6 13  0
  subtype7  4  1
  subtype8  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    1
  subtype2    9    0
  subtype3    8    0
  subtype4   14    1
  subtype5   18    1
  subtype6   13    0
  subtype7    4    1
  subtype8    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       10        9        8       14       18       13        4        8
  1        1        0        0        1        1        0        1        0
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1  4  9
  subtype2  4  9
  subtype3  2  4
  subtype4  3 10
  subtype5  4 12
  subtype6  4  8
  subtype7  3  4
  subtype8  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    9
  subtype2    4    9
  subtype3    2    4
  subtype4    3   10
  subtype5    4   12
  subtype6    4    8
  subtype7    3    4
  subtype8    4    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         4        4        2        3        4        4        3        4
  YES        9        9        4       10       12        8        4        2
[1] 2 8
[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                               21
  subtype2             0                               25
  subtype3             1                               15
  subtype4             0                               20
  subtype5             1                               18
  subtype6             0                               27
  subtype7             0                                7
  subtype8             0                               11
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             0
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             2
  subtype6                                             0
  subtype7                                             0
  subtype8                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   2
  subtype2                                   1
  subtype3                                   3
  subtype4                                   1
  subtype5                                   8
  subtype6                                   0
  subtype7                                   0
  subtype8                                   1
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         2
  subtype6                                         0
  subtype7                                         0
  subtype8                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            1
  subtype2                                            0
  subtype3                                            1
  subtype4                                            0
  subtype5                                            2
  subtype6                                            0
  subtype7                                            0
  subtype8                                            0
D3V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        1
  CERVICAL SQUAMOUS CELL CARCINOMA                    21       25       15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  2        1        3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        0        1
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    20       18       27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  1        8        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        2        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        2        0
                                               clus
vv                                              subtype7 subtype8
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                     7       11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0
[1] 6 8
[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                                0     2                         3
  subtype2                                0     1                         4
  subtype3                                0     1                         2
  subtype4                                0     1                         0
  subtype5                                0     4                         1
  subtype6                                2     4                         1
  subtype7                                0     1                         1
  subtype8                                1     1                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    19
  subtype2                                         0    21
  subtype3                                         0    15
  subtype4                                         0    16
  subtype5                                         0    23
  subtype6                                         0    18
  subtype7                                         0     5
  subtype8                                         0     8
D3V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        0        0
  ASIAN                                            2        1        1        1
  BLACK OR AFRICAN AMERICAN                        3        4        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           19       21       15       16
                                           clus
vv                                          subtype5 subtype6 subtype7 subtype8
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        0        1
  ASIAN                                            4        4        1        1
  BLACK OR AFRICAN AMERICAN                        1        1        1        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        0
  WHITE                                           23       18        5        8
[1] 5 8
[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 22
  subtype2  2 15
  subtype3  0 15
  subtype4  3 11
  subtype5  0 23
  subtype6  4 17
  subtype7  1  3
  subtype8  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   22
  subtype2    2   15
  subtype3    0   15
  subtype4    3   11
  subtype5    0   23
  subtype6    4   17
  subtype7    1    3
  subtype8    2    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        0        3        0        4
  NOT HISPANIC OR LATINO       22       15       15       11       23       17
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            1        2
  NOT HISPANIC OR LATINO        3        7
[1] 2 8
[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 17  7
  subtype2 15  9
  subtype3 11  4
  subtype4 15  2
  subtype5 21  7
  subtype6 20  3
  subtype7  6  1
  subtype8  6  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    7
  subtype2   15    9
  subtype3   11    4
  subtype4   15    2
  subtype5   21    7
  subtype6   20    3
  subtype7    6    1
  subtype8    6    2
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  TUMOR FREE       17       15       11       15       21       20        6
  WITH TUMOR        7        9        4        2        7        3        1
            clus
vv           subtype8
  TUMOR FREE        6
  WITH TUMOR        2
[1] 2 8
[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  7 13  0  3
  subtype2  1  9 15  1  0
  subtype3  1 11  5  0  2
  subtype4  0  9 12  0  0
  subtype5  1 14 16  0  1
  subtype6  4 13  7  0  1
  subtype7  0  4  2  0  0
  subtype8  0  8  4  0  1
D3V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  G1        3        1        1        0        1        4        0        0
  G2        7        9       11        9       14       13        4        8
  G3       13       15        5       12       16        7        2        4
  G4        0        1        0        0        0        0        0        0
  GX        3        0        2        0        1        1        0        1
[1] 5 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
       5        6        3        2        8        4        3 
 [1] "subtype1" "subtype3" "subtype5" "subtype5" "subtype1" "subtype5"
 [7] "subtype2" "subtype5" "subtype8" "subtype1" "subtype2" "subtype5"
[13] "subtype6" "subtype8" "subtype5" "subtype2" "subtype6" "subtype2"
[19] "subtype1" "subtype2" "subtype8" "subtype5" "subtype3" "subtype3"
[25] "subtype5" "subtype2" "subtype1" "subtype6" "subtype6"
D3V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           2
  subtype2                                           6
  subtype3                                           5
  subtype4                                           4
  subtype5                                           6
  subtype6                                           2
  subtype7                                           0
  subtype8                                           3
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      0
  subtype3                                      0
  subtype4                                      0
  subtype5                                      2
  subtype6                                      2
  subtype7                                      0
  subtype8                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              2
  subtype2                                               0              4
  subtype3                                               0              3
  subtype4                                               0              3
  subtype5                                               0              5
  subtype6                                               1              4
  subtype7                                               1              0
  subtype8                                               0              2
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  15
  subtype2                  10
  subtype3                   7
  subtype4                  11
  subtype5                  18
  subtype6                  15
  subtype7                   5
  subtype8                   5
D3V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            2        6        5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        0        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        0        0
  CURRENT SMOKER                                         2        4        3
  LIFELONG NON-SMOKER                                   15       10        7
                                                 clus
vv                                                subtype4 subtype5 subtype6
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            4        6        2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        0        1
  CURRENT SMOKER                                         3        5        4
  LIFELONG NON-SMOKER                                   11       18       15
                                                 clus
vv                                                subtype7 subtype8
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            0        3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0
  CURRENT SMOKER                                         0        2
  LIFELONG NON-SMOKER                                    5        5
[1] 5 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V18, continuous
D3V19, binary
          cls
clus       0 1
  subtype1 3 1
  subtype2 5 1
  subtype3 2 0
  subtype4 4 0
  subtype5 6 0
  subtype6 1 0
  subtype7 0 0
  subtype8 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    5    1
  subtype3    2    0
  subtype4    4    0
  subtype5    6    0
  subtype6    1    0
  subtype7    0    0
  subtype8    0    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMPLETED AS PLANNED           3        5        2        4        6        1
  TREATMENT NOT COMPLETED        1        1        0        0        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"
D3V20, continuous
D3V21, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      10       11        8       10       14       14        2        3 
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype5" "subtype2"
 [7] "subtype3" "subtype6" "subtype2" "subtype5" "subtype5" "subtype1"
[13] "subtype5" "subtype5" "subtype2" "subtype3" "subtype5" "subtype2"
[19] "subtype2" "subtype5" "subtype4" "subtype6" "subtype5" "subtype1"
[25] "subtype3" "subtype1" "subtype4" "subtype6" "subtype1" "subtype6"
[31] "subtype3" "subtype4" "subtype6" "subtype5" "subtype6" "subtype4"
[37] "subtype4" "subtype6" "subtype1" "subtype2" "subtype1" "subtype6"
[43] "subtype6" "subtype1" "subtype4" "subtype5" "subtype1" "subtype5"
[49] "subtype5" "subtype3" "subtype6" "subtype5" "subtype6" "subtype1"
[55] "subtype2" "subtype6" "subtype8" "subtype8" "subtype3" "subtype8"
[61] "subtype2" "subtype5" "subtype2" "subtype4" "subtype6" "subtype2"
[67] "subtype6" "subtype4" "subtype3" "subtype4"
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      11       11        8       11       14       14        2        3 
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype5" "subtype2"
 [7] "subtype3" "subtype6" "subtype2" "subtype5" "subtype5" "subtype1"
[13] "subtype5" "subtype5" "subtype2" "subtype3" "subtype5" "subtype2"
[19] "subtype2" "subtype5" "subtype4" "subtype6" "subtype5" "subtype1"
[25] "subtype3" "subtype1" "subtype4" "subtype6" "subtype1" "subtype6"
[31] "subtype3" "subtype4" "subtype6" "subtype5" "subtype6" "subtype4"
[37] "subtype4" "subtype6" "subtype1" "subtype2" "subtype1" "subtype6"
[43] "subtype6" "subtype1" "subtype4" "subtype5" "subtype1" "subtype5"
[49] "subtype5" "subtype3" "subtype6" "subtype5" "subtype6" "subtype1"
[55] "subtype2" "subtype6" "subtype8" "subtype8" "subtype3" "subtype8"
[61] "subtype2" "subtype5" "subtype2" "subtype4" "subtype6" "subtype2"
[67] "subtype6" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   1
  subtype7                                   0
  subtype8                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       2
  subtype2                                   3                       5
  subtype3                                   0                       2
  subtype4                                   0                       5
  subtype5                                   3                       5
  subtype6                                   0                       5
  subtype7                                   0                       1
  subtype8                                   0                       0
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       0
  subtype2                       1                       1
  subtype3                       0                       1
  subtype4                       0                       0
  subtype5                       0                       2
  subtype6                       0                       1
  subtype7                       0                       0
  subtype8                       0                       0
D3V26, multiclass
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       5       10        3        5       10        7        1 
 [1] "subtype1" "subtype1" "subtype5" "subtype3" "subtype6" "subtype2"
 [7] "subtype5" "subtype5" "subtype5" "subtype3" "subtype5" "subtype2"
[13] "subtype2" "subtype5" "subtype1" "subtype1" "subtype4" "subtype2"
[19] "subtype4" "subtype6" "subtype3" "subtype4" "subtype6" "subtype5"
[25] "subtype6" "subtype2" "subtype4" "subtype4" "subtype5" "subtype2"
[31] "subtype6" "subtype5" "subtype1" "subtype6" "subtype2" "subtype5"
[37] "subtype2" "subtype6" "subtype2" "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        0        0
  OTHER LOCATION, SPECIFY                    2        5        2        5
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    0        1        1        0
                                     clus
vv                                    subtype5 subtype6
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        3        0
  OTHER LOCATION, SPECIFY                    5        5
  POSITIVE BLADDER MARGIN                    0        0
  POSITIVE VAGINAL MARGIN                    2        1
[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                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             1
  subtype6                                             1
  subtype7                                             0
  subtype8                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              2
  subtype2                                              2
  subtype3                                              0
  subtype4                                              1
  subtype5                                              5
  subtype6                                              2
  subtype7                                              1
  subtype8                                              0
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 8
  subtype2                                                                                 4
  subtype3                                                                                 2
  subtype4                                                                                 7
  subtype5                                                                                 9
  subtype6                                                                                10
  subtype7                                                                                 2
  subtype8                                                                                 4
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           14
  subtype2                                                                                           13
  subtype3                                                                                           13
  subtype4                                                                                           10
  subtype5                                                                                           14
  subtype6                                                                                            9
  subtype7                                                                                            2
  subtype8                                                                                            4
D3V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       14
                                                                                              clus
vv                                                                                             subtype2
  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)       13
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       13
                                                                                              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)                   7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       10
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       14
                                                                                              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)                  10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        9
                                                                                              clus
vv                                                                                             subtype7
  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)                   2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        2
                                                                                              clus
vv                                                                                             subtype8
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        4
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V28, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2  5 11
  subtype3  7  5
  subtype4  6  8
  subtype5  7 19
  subtype6  9  7
  subtype7  1  1
  subtype8  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2    5   11
  subtype3    7    5
  subtype4    6    8
  subtype5    7   19
  subtype6    9    7
  subtype7    1    1
  subtype8    8    2
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  ABSENT         9        5        7        6        7        9        1
  PRESENT        7       11        5        8       19        7        1
         clus
vv        subtype8
  ABSENT         8
  PRESENT        2
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V29, continuous
D3V30, continuous
D3V31, binary
          cls
clus        0  1
  subtype1  9 14
  subtype2  7 11
  subtype3  3  7
  subtype4  4  9
  subtype5  5 11
  subtype6  9 14
  subtype7  1  2
  subtype8  1  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   14
  subtype2    7   11
  subtype3    3    7
  subtype4    4    9
  subtype5    5   11
  subtype6    9   14
  subtype7    1    2
  subtype8    1    8
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            9        7        3        4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       14       11        7        9
                                          clus
vv                                         subtype5 subtype6 subtype7 subtype8
  KERATINIZING SQUAMOUS CELL CARCINOMA            5        9        1        1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       11       14        2        8
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           4          7
  subtype2            1           7          8
  subtype3            2           3          3
  subtype4            1           4          8
  subtype5            1           9         10
  subtype6            0           4          9
  subtype7            0           0          3
  subtype8            0           1          3
D3V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CURRENT USER        0        1        2        1        1        0        0
  FORMER USER         4        7        3        4        9        4        0
  NEVER USED          7        8        3        8       10        9        3
              clus
vv             subtype8
  CURRENT USER        0
  FORMER USER         1
  NEVER USED          3
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V34, continuous
D3V35, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2 10  1
  subtype3 10  1
  subtype4 11  2
  subtype5 20  3
  subtype6 13  2
  subtype7  2  0
  subtype8  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   10    1
  subtype3   10    1
  subtype4   11    2
  subtype5   20    3
  subtype6   13    2
  subtype7    2    0
  subtype8    7    2
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  ABSENT        11       10       10       11       20       13        2
  PRESENT        1        1        1        2        3        2        0
         clus
vv        subtype8
  ABSENT         7
  PRESENT        2
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         9     1
  subtype2           1         8     0
  subtype3           0         3     0
  subtype4           0        10     0
  subtype5           1         8     0
  subtype6           1         6     0
  subtype7           0         3     0
  subtype8           0         1     0
D3V36, multiclass
[1] "Remove cluster labels:" "subtype8"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      10        9        3       10        9        7        3        1 
 [1] "subtype1" "subtype2" "subtype1" "subtype5" "subtype2" "subtype5"
 [7] "subtype2" "subtype5" "subtype4" "subtype6" "subtype1" "subtype2"
[13] "subtype4" "subtype4" "subtype4" "subtype6" "subtype6" "subtype2"
[19] "subtype4" "subtype4" "subtype5" "subtype6" "subtype1" "subtype2"
[25] "subtype5" "subtype2" "subtype1" "subtype1" "subtype1" "subtype5"
[31] "subtype5" "subtype6" "subtype4" "subtype6" "subtype4" "subtype6"
[37] "subtype2" "subtype7" "subtype3" "subtype1" "subtype1" "subtype5"
[43] "subtype1" "subtype3" "subtype7" "subtype3" "subtype2" "subtype4"
[49] "subtype4" "subtype7" "subtype5"
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CARBOPLATIN        0        1        0        0        1        1        0
  CISPLATIN          9        8        3       10        8        6        3
  OTHER              1        0        0        0        0        0        0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V37, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"               "subtype7"              
[7] "subtype8"              
clus
subtype1 subtype2 subtype3 subtype4 subtype6 subtype7 subtype8 
       1        2        1        1        4        1        1 
[1] "subtype6" "subtype6" "subtype6" "subtype6"
D3V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       2        1         1         0        3         5         8
  subtype2       0        0         0         0        5         5         6
  subtype3       0        0         0         0        3         7         3
  subtype4       0        0         0         1        5         9         0
  subtype5       1        0         0         0        4        10         6
  subtype6       0        0         0         0        3         7         3
  subtype7       0        0         0         0        3         1         0
  subtype8       1        0         0         0        1         4         2
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         0          0          0         2         0
  subtype2        0         0          1          2         3         0
  subtype3        0         1          0          0         3         0
  subtype4        2         0          0          0         3         0
  subtype5        0         1          1          1         1         0
  subtype6        1         1          2          0         3         1
  subtype7        0         1          0          0         0         0
  subtype8        1         1          0          1         1         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          3         0         1
  subtype2          0          2         1         0
  subtype3          0          2         0         0
  subtype4          0          1         0         0
  subtype5          0          5         1         1
  subtype6          0          5         1         0
  subtype7          1          0         1         0
  subtype8          0          1         0         0
D3V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           2        0        0        0        1        0        0
  STAGE IA          1        0        0        0        0        0        0
  STAGE IA1         1        0        0        0        0        0        0
  STAGE IA2         0        0        0        1        0        0        0
  STAGE IB          3        5        3        5        4        3        3
  STAGE IB1         5        5        7        9       10        7        1
  STAGE IB2         8        6        3        0        6        3        0
  STAGE II          0        0        0        2        0        1        0
  STAGE IIA         0        0        1        0        1        1        1
  STAGE IIA1        0        1        0        0        1        2        0
  STAGE IIA2        0        2        0        0        1        0        0
  STAGE IIB         2        3        3        3        1        3        0
  STAGE III         0        0        0        0        0        1        0
  STAGE IIIA        0        0        0        0        0        0        1
  STAGE IIIB        3        2        2        1        5        5        0
  STAGE IVA         0        1        0        0        1        1        1
  STAGE IVB         1        0        0        0        1        0        0
            clus
vv           subtype8
  STAGE I           1
  STAGE IA          0
  STAGE IA1         0
  STAGE IA2         0
  STAGE IB          1
  STAGE IB1         4
  STAGE IB2         2
  STAGE II          1
  STAGE IIA         1
  STAGE IIA1        0
  STAGE IIA2        1
  STAGE IIB         1
  STAGE III         0
  STAGE IIIA        0
  STAGE IIIB        1
  STAGE IVA         0
  STAGE IVB         0
[1] 17  8
[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 39  7
  subtype3 40  8
  subtype4 14  6
  subtype5 14  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       46       48       20       17 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        7        8        6        3 
$subtype1
TCGA-2W-A8YY TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A3HE 
       17.52        11.44       144.16        46.32        38.99        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7X3 TCGA-EA-A1QS TCGA-EA-A3QE TCGA-EA-A5FO 
       17.85        20.42         9.34        39.55        25.02        26.79 
TCGA-EA-A5ZD TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2R8 TCGA-EX-A449 TCGA-EX-A69L 
       27.29         0.36        26.27         1.45        14.70        19.79 
TCGA-FU-A40J TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LF TCGA-LP-A4AW 
       14.01        17.75        16.57        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        14.60        19.13 

$subtype2
TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MP TCGA-C5-A2LT 
       17.82        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        95.67 
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        36.89        26.40 
TCGA-EA-A556 TCGA-EK-A2IR TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2RC TCGA-EK-A2RD 
       14.89       113.16         0.39         0.59         4.31         0.10 
TCGA-EK-A2RL TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3TX TCGA-IR-A3LA 
       47.77         8.32        15.55        19.04         1.48       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JX-A5QV TCGA-LP-A5U2 
       66.81       129.37        81.96        29.85        20.91         0.30 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A73P 
       22.52        17.82        28.08        19.96        20.84        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-VS-A9UQ TCGA-WL-A834 
       18.64        22.62        41.52        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        14.73        82.06        63.98        69.96 
TCGA-DS-A1O9 TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
        8.75        12.36       127.36        40.87        37.35        31.53 
TCGA-EA-A3HU TCGA-EA-A44S TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       33.30         0.30        25.91        27.25        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2RK TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23K 
       60.72         0.43         0.43         0.49        20.35         1.22 
TCGA-FU-A3TQ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U3 
       26.14        14.93        36.36        15.58       209.59         0.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-Q1-A6DW TCGA-UC-A7PF 
       19.56         8.35         8.52        11.38        17.56        93.99 
TCGA-VS-A8EK TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9V0 
       27.25        59.18        16.64        50.47        24.30        18.84 

$subtype4
TCGA-C5-A1M6 TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A8XI TCGA-DS-A0VK 
       31.40        40.93        73.45        78.35         8.35        36.76 
TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A50E 
       55.63         8.28        31.36        24.56        26.01         7.46 
TCGA-EK-A2IP TCGA-EK-A3GN TCGA-IR-A3LH TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 
        6.64         0.03        78.71        21.11        12.49        17.23 
TCGA-Q1-A73Q TCGA-VS-A9UB 
        9.34        29.95 

$subtype5
TCGA-C5-A1MJ TCGA-DS-A1OA TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A4BA 
        0.46        28.90        17.52        30.90        31.73        24.82 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A3GM TCGA-FU-A23L 
       27.22         0.36         0.13        40.96         0.76        23.84 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-LP-A7HU TCGA-ZJ-AAXA 
       35.44        25.41       147.39        13.35         1.41 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.36     0.10     0.30     0.03     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
  144.16   210.67   209.59    78.71   147.39 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.575   22.800   26.695   25.285   24.820 
[1] "0.4 - 144.2 (18.6)" "0.1 - 210.7 (22.8)" "0.3 - 209.6 (26.7)"
[4] "0.0 - 78.7 (25.3)"  "0.1 - 147.4 (24.8)"
D4V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 19  4  0  0
  subtype2 31  9  2  0
  subtype3 24 11  4  2
  subtype4 13  3  1  1
  subtype5 12  5  0  0
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       19       31       24       13       12
  T2        4        9       11        3        5
  T3        0        2        4        1        0
  T4        0        0        2        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 30 12
  subtype3 19 14
  subtype4 13  6
  subtype5 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   30   12
  subtype3   19   14
  subtype4   13    6
  subtype5   14    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       17       30       19       13       14
  1        4       12       14        6        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 24  1
  subtype3 26  1
  subtype4 12  1
  subtype5 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   24    1
  subtype3   26    1
  subtype4   12    1
  subtype5   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12       24       26       12       10
  1        1        1        1        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1  7 10
  subtype2 10 15
  subtype3  6 24
  subtype4  3  6
  subtype5  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   10
  subtype2   10   15
  subtype3    6   24
  subtype4    3    6
  subtype5    2    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7       10        6        3        2
  YES       10       15       24        6        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               26
  subtype2             2                               35
  subtype3             0                               49
  subtype4             0                               23
  subtype5             0                               11
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   2
  subtype2                                   8
  subtype3                                   1
  subtype4                                   0
  subtype5                                   5
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         2
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            1
  subtype2                                            1
  subtype3                                            1
  subtype4                                            0
  subtype5                                            1
D4V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    26       35       49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  2        8        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        2        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        1        1
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    23       11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        1
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       15       14        6        2 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype4" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
[37] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype3"
D4V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         3
  subtype2                                2     1                         2
  subtype3                                1     4                         3
  subtype4                                0     2                         4
  subtype5                                0     4                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    23
  subtype2                                         0    37
  subtype3                                         0    37
  subtype4                                         0    15
  subtype5                                         0    13
D4V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        1        0
  ASIAN                                            4        1        4        2
  BLACK OR AFRICAN AMERICAN                        3        2        3        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           23       37       37       15
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 0
  ASIAN                                            4
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           13
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
          cls
clus        0  1
  subtype1  1 28
  subtype2  3 29
  subtype3  6 29
  subtype4  1 14
  subtype5  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   28
  subtype2    3   29
  subtype3    6   29
  subtype4    1   14
  subtype5    2   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        3        6        1        2
  NOT HISPANIC OR LATINO       28       29       29       14       13
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
D4V13, binary
          cls
clus        0  1
  subtype1 23  6
  subtype2 33  8
  subtype3 34  9
  subtype4 12  7
  subtype5  9  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    6
  subtype2   33    8
  subtype3   34    9
  subtype4   12    7
  subtype5    9    5
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       23       33       34       12        9
  WITH TUMOR        6        8        9        7        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  2 15 12  0  3
  subtype2  5 16 26  0  2
  subtype3  2 26 17  0  2
  subtype4  1  9 10  1  1
  subtype5  0  9  9  0  0
D4V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        2        5        2        1        0
  G2       15       16       26        9        9
  G3       12       26       17       10        9
  G4        0        0        0        1        0
  GX        3        2        2        1        0
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       11       10        1        3 
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype5" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype5" "subtype2" "subtype3"
[19] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[25] "subtype3" "subtype3" "subtype2" "subtype1" "subtype5" "subtype3"
D4V16, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       15       14        6        2 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype4" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
[37] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype3"
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           3
  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
D4V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3       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"
D4V18, continuous
D4V19, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 6 0
  subtype3 7 1
  subtype4 3 0
  subtype5 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    6    0
  subtype3    7    1
  subtype4    3    0
  subtype5    0    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           5        6        7        3
  TREATMENT NOT COMPLETED        1        0        1        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V20, continuous
D4V21, continuous
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       3
  subtype2                                   4                      10
  subtype3                                   2                       7
  subtype4                                   0                       3
  subtype5                                   0                       2
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       0
  subtype2                       0                       2
  subtype3                       0                       1
  subtype4                       1                       2
  subtype5                       0                       0
D4V26, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       17       10        6        2 
 [1] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype4" "subtype3"
[19] "subtype2" "subtype4" "subtype4" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype2" "subtype4" "subtype2"
[31] "subtype3" "subtype1" "subtype3" "subtype4" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        4        2        0
  OTHER LOCATION, SPECIFY                    3       10        7        3
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    0        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                                                                                           19
  subtype2                                                                                           23
  subtype3                                                                                           18
  subtype4                                                                                           12
  subtype5                                                                                            7
D4V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       19
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       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"
D4V28, binary
          cls
clus        0  1
  subtype1 13  8
  subtype2 13 22
  subtype3 12 17
  subtype4  6  6
  subtype5  8  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    8
  subtype2   13   22
  subtype3   12   17
  subtype4    6    6
  subtype5    8    7
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        13       13       12        6        8
  PRESENT        8       22       17        6        7
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V29, continuous
D4V30, continuous
D4V31, binary
          cls
clus        0  1
  subtype1  7 18
  subtype2 16 14
  subtype3 10 25
  subtype4  6 11
  subtype5  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   18
  subtype2   16   14
  subtype3   10   25
  subtype4    6   11
  subtype5    0    8
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            7       16       10        6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       18       14       25       11
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA            0
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        8
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0           4          8
  subtype2            3          12         13
  subtype3            1           6         18
  subtype4            0           6          8
  subtype5            1           4          4
D4V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        0        3        1        0        1
  FORMER USER         4       12        6        6        4
  NEVER USED          8       13       18        8        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V34, continuous
D4V35, binary
          cls
clus        0  1
  subtype1 16  1
  subtype2 24  3
  subtype3 25  3
  subtype4  9  1
  subtype5 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    1
  subtype2   24    3
  subtype3   25    3
  subtype4    9    1
  subtype5   10    4
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        16       24       25        9       10
  PRESENT        1        3        3        1        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         9     1
  subtype2           1        10     0
  subtype3           0        22     0
  subtype4           0         6     0
  subtype5           2         1     0
D4V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        0        1        0        0        2
  CISPLATIN          9       10       22        6        1
  OTHER              1        0        0        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V37, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        5        2        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D4V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        4         7         9
  subtype2       1        0         0         0        8        20         8
  subtype3       1        0         0         1        8        10         4
  subtype4       1        0         0         0        5         5         3
  subtype5       0        0         0         0        2         6         4
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         1          0          0         3         0
  subtype2        0         1          1          2         3         0
  subtype3        2         1          0          0         8         1
  subtype4        0         1          1          1         2         0
  subtype5        2         1          2          1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          3         0         1
  subtype2          0          3         0         1
  subtype3          1         10         3         0
  subtype4          0          3         1         0
  subtype5          0          0         0         0
D4V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        1        1        0
  STAGE IA          1        0        0        0        0
  STAGE IA1         1        0        0        0        0
  STAGE IA2         0        0        1        0        0
  STAGE IB          4        8        8        5        2
  STAGE IB1         7       20       10        5        6
  STAGE IB2         9        8        4        3        4
  STAGE II          0        0        2        0        2
  STAGE IIA         1        1        1        1        1
  STAGE IIA1        0        1        0        1        2
  STAGE IIA2        0        2        0        1        1
  STAGE IIB         3        3        8        2        0
  STAGE III         0        0        1        0        0
  STAGE IIIA        0        0        1        0        0
  STAGE IIIB        3        3       10        3        0
  STAGE IVA         0        0        3        1        0
  STAGE IVB         1        1        0        0        0
[1] 17  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 42 12
  subtype2 76 23
  subtype3 53 15
  subtype4 45 21
subtype1 subtype2 subtype3 subtype4 
      54       99       68       66 
subtype1 subtype2 subtype3 subtype4 
      12       23       15       21 
$subtype1
TCGA-2W-A8YY TCGA-BI-A0VS TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LX TCGA-C5-A7CK 
       17.52        57.04        35.61        20.91        83.05       134.33 
TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DS-A0VK TCGA-DS-A1O9 
      146.86        23.51        20.81        20.91        36.76         8.75 
TCGA-DS-A1OB TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A410 
       28.31       127.36        22.98        39.55        13.05        26.40 
TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2GZ 
       31.73        24.82        14.89        27.25        27.22        12.59 
TCGA-EK-A2IR TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EX-A1H5 TCGA-FU-A3HZ 
      113.16        19.27         0.59         0.13        20.35        36.26 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A57G TCGA-HM-A3JK TCGA-HM-A6W2 
       20.98         1.48        16.14        35.44        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        22.62        46.52        19.96 
TCGA-VS-A954 TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UT 
       56.35        43.40        24.30        14.53        47.47        15.85 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       17.82        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        63.98        87.75        58.88        55.63 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       28.90        16.83        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 
       31.36        33.30        25.02         0.30         7.46        25.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2RA 
       27.29        24.00        13.48         0.36         1.51        40.96 
TCGA-EK-A2RK TCGA-EK-A2RN TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ 
        0.43         0.53        23.84        19.04        31.36        26.14 
TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VJ 
       28.31        10.55        21.67        14.93        36.36        21.44 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A5U3 TCGA-MA-AA3W 
        8.28        18.15       209.59        20.91         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF 
       19.56        19.56         8.52        28.08        19.96        20.84 
TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EH 
       16.41        17.56        93.99        12.16        45.57        32.42 
TCGA-VS-A8EK TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       27.25        32.15        11.51        59.18        31.27        40.87 
TCGA-VS-A94Z TCGA-VS-A9U7 TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV 
       33.37        48.39        45.11        27.25        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAX4 
       18.25        18.25        17.75        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        95.11        82.06        16.18 
TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A5FO TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2RC 
       17.52        24.56        26.79         0.39         0.36         4.31 
TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M 
       47.77         0.49         0.76         7.92        14.70         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A770 TCGA-HG-A2PA 
       15.55         1.22        16.11        14.01         1.12        25.41 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
      147.39       137.16        66.81       129.37        96.95        81.96 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       28.37        44.61        54.81        15.58        15.95        16.14 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH 
       15.88        18.64        14.60        69.50        36.13        39.78 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UJ 
       58.45        55.50        51.32        50.47        27.12         1.71 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       47.87        41.52        26.07        67.20        18.84         5.16 
TCGA-VS-A9V4 TCGA-VS-A9V5 
        4.34        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        14.73        69.96        95.67        12.36         8.28 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       36.89        26.01        60.72        26.27         6.64         0.43 
TCGA-EK-A2R8 TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-GH-A9DA 
        1.45         0.10         0.03        15.22        19.79        17.75 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JX-A3PZ 
       78.71        29.85        27.42        24.56        15.58        21.11 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MY-A913 
       11.28        12.49        17.82         8.35        11.38        17.23 
TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI 
        9.04        14.07        19.59        11.67        10.03        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 
       65.49        53.59        16.64         4.73        40.14        15.68 
TCGA-VS-A958 TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       50.14        29.95        46.92        15.42        67.59        19.13 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.16     0.36     0.03 
subtype1 subtype2 subtype3 subtype4 
  146.86   210.67   147.39   154.32 
subtype1 subtype2 subtype3 subtype4 
  21.800   26.140   24.985   19.360 
[1] "0.1 - 146.9 (21.8)" "0.2 - 210.7 (26.1)" "0.4 - 147.4 (25.0)"
[4] "0.0 - 154.3 (19.4)"
D5V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 23 14  6  3
  subtype2 48 27  7  4
  subtype3 40 14  2  1
  subtype4 29 16  5  2
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       23       48       40       29
  T2       14       27       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 23 12
  subtype2 46 27
  subtype3 35 10
  subtype4 29 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   12
  subtype2   46   27
  subtype3   35   10
  subtype4   29   11
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       23       46       35       29
  1       12       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 24  4
  subtype2 43  1
  subtype3 23  2
  subtype4 26  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    4
  subtype2   43    1
  subtype3   23    2
  subtype4   26    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       24       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"
D5V6, binary
          cls
clus        0  1
  subtype1  9 24
  subtype2 18 38
  subtype3 15 30
  subtype4 15 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   24
  subtype2   18   38
  subtype3   15   30
  subtype4   15   33
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         9       18       15       15
  YES       24       38       30       33
[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                               47
  subtype2             0                              105
  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                                  18
  subtype4                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         1
  subtype2                                         0
  subtype3                                         2
  subtype4                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            2
  subtype2                                            0
  subtype3                                           15
  subtype4                                            0
D5V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    47      105       28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        2        0        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  3        0       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            1        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         2        0       15
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    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"
D5V8, continuous
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     7                         7
  subtype2                                1     7                        11
  subtype3                                0     2                         1
  subtype4                                4     4                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    36
  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                                            7        7        2        4
  BLACK OR AFRICAN AMERICAN                        7       11        1       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           36       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 39
  subtype2  8 58
  subtype3  5 32
  subtype4  9 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   39
  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       39       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 33 20
  subtype2 70 21
  subtype3 43 17
  subtype4 43 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   20
  subtype2   70   21
  subtype3   43   17
  subtype4   43   20
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       33       70       43       43
  WITH TUMOR       20       21       17       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  2 22 30  0  2
  subtype2  7 62 28  0  6
  subtype3  7 30 25  0  7
  subtype4  2 21 35  1  9
D5V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        2        7        7        2
  G2       22       62       30       21
  G3       30       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"
D5V15, continuous
D5V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  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                  22
  subtype2                  48
  subtype3                  39
  subtype4                  35
D5V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7       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                                   22       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"
D5V18, continuous
D5V19, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2 10  1
  subtype3  4  0
  subtype4  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   10    1
  subtype3    4    0
  subtype4    8    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           7       10        4        8
  TREATMENT NOT COMPLETED        0        1        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V20, continuous
D5V21, continuous
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       4
  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
D5V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        2        3
  OTHER LOCATION, SPECIFY                    4       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                                                                                21
  subtype2                                                                                35
  subtype3                                                                                19
  subtype4                                                                                 7
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           21
  subtype2                                                                                           38
  subtype3                                                                                           30
  subtype4                                                                                           35
D5V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       21
                                                                                              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"
D5V28, binary
          cls
clus        0  1
  subtype1 13 19
  subtype2 26 29
  subtype3 18 21
  subtype4 14 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   19
  subtype2   26   29
  subtype3   18   21
  subtype4   14   10
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        13       26       18       14
  PRESENT       19       29       21       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V29, continuous
D5V30, continuous
D5V31, binary
          cls
clus        0  1
  subtype1 15 21
  subtype2 21 54
  subtype3  1 16
  subtype4 18 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   21
  subtype2   21   54
  subtype3    1   16
  subtype4   18   28
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA           15       21        1       18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       21       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"
D5V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0          12         20
  subtype2            3          15         31
  subtype3            8          15         18
  subtype4            4          11         20
D5V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        0        3        8        4
  FORMER USER        12       15       15       11
  NEVER USED         20       31       18       20
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V34, continuous
D5V35, binary
          cls
clus        0  1
  subtype1 18  5
  subtype2 32 10
  subtype3 28  4
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    5
  subtype2   32   10
  subtype3   28    4
  subtype4   21    0
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        18       32       28       21
  PRESENT        5       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           3        16     0
  subtype2           2        34     0
  subtype3           1        20     1
  subtype4           1        32     1
D5V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  CARBOPLATIN        3        2        1        1
  CISPLATIN         16       34       20       32
  OTHER              0        0        1        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V37, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        9        1        4 
 [1] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
 [7] "subtype4" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2"
D5V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        1         1         0        5        13         8
  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        13         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
D5V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        1        2
  STAGE IA          1        0        0        0
  STAGE IA1         1        0        0        0
  STAGE IA2         0        1        0        0
  STAGE IB          5       15        5       13
  STAGE IB1        13       22       31       11
  STAGE IB2         8       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       13       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  53  17
  subtype2 141  41
  subtype3  22  13
subtype1 subtype2 subtype3 
      70      182       35 
subtype1 subtype2 subtype3 
      17       41       13 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ 
       17.52        31.40        35.01        57.73        35.61         0.46 
TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X8 
       44.22        38.43        33.24        18.02        20.35         2.73 
TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH 
       20.81         1.12        95.11        82.06        16.18        17.52 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF 
       26.40        31.73        24.82        14.89        26.79        27.22 
TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EX-A1H6 TCGA-EX-A449 
        0.36        47.77         0.49         0.76         7.92        14.70 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G 
       15.55         1.22        16.11        36.26        14.01        35.44 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI 
        1.12         9.44       137.16        66.81        96.95        81.96 
TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-PN-A8MA 
        3.29        28.37        44.61        13.35        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        18.64        22.62        69.50 
TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL 
       19.96        36.13        39.78        58.45         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UZ 
       47.87        47.47        41.52        26.07        15.85        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16         4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI 
       17.82        49.48        57.04        23.67        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       46.32        30.21        38.99         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A3HL 
        3.58        83.05        78.35       100.14        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
      210.67       154.32       101.82       134.33        15.48       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
      155.77       131.11        94.95        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-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        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
       69.96        95.67         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        40.87        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         0.30         7.46        25.91        27.29        27.25 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       24.00        13.48         0.36        12.59        60.72         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-A2RC TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 
       40.96         4.31         0.43         0.53         0.10        20.35 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI 
       19.79         8.32        23.84        19.04        31.36        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA 
       26.14         1.48        16.14        28.31        10.55        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK 
       21.67        20.78        14.93       147.39       129.37        29.85 
TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       36.36        24.56        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
       18.15       209.59        20.91        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE 
        8.52        11.38        28.08        34.62        19.96        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O 
       20.84        16.41        15.95         9.04        17.56        14.07 
TCGA-Q1-A73Q TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EC 
        9.34        19.59        14.60        93.99        12.16        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        27.25        65.49        32.15 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 
       11.51        59.18        31.27        40.87        33.37        40.14 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       43.40        48.39        27.12        24.30        46.92        45.11 
TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 TCGA-VS-A9V3 
       27.25        14.53         3.42        18.25        18.25        17.75 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       26.01        29.26        67.59        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

$subtype3
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MQ TCGA-C5-A2LT 
       11.44        18.74         5.46        53.16        33.90        73.18 
TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A8XK TCGA-C5-A8YR 
       73.45        52.01        17.19         9.34        99.91        27.52 
TCGA-C5-A902 TCGA-C5-A907 TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H1 
        4.90        14.73         8.28        36.89        26.01        26.27 
TCGA-EK-A2PK TCGA-EK-A2R8 TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-GH-A9DA TCGA-IR-A3LH 
        0.39         1.45         0.03        15.22        17.75        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        17.23        11.67        10.03 
TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-AA62 
       53.59        16.64         4.73        29.95        15.42 

subtype1 subtype2 subtype3 
    0.36     0.10     0.03 
subtype1 subtype2 subtype3 
  137.16   210.67    99.91 
subtype1 subtype2 subtype3 
   20.58    24.79    17.23 
[1] "0.4 - 137.2 (20.6)" "0.1 - 210.7 (24.8)" "0.0 - 99.9 (17.2)" 
D6V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 39 20  3  2
  subtype2 86 42 16  8
  subtype3 15  9  1  0
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       39       86       15
  T2       20       42        9
  T3        3       16        1
  T4        2        8        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 38 13
  subtype2 78 42
  subtype3 17  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   13
  subtype2   78   42
  subtype3   17    5
   clus
vv  subtype1 subtype2 subtype3
  0       38       78       17
  1       13       42        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 27  5
  subtype2 77  3
  subtype3 12  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    5
  subtype2   77    3
  subtype3   12    2
   clus
vv  subtype1 subtype2 subtype3
  0       27       77       12
  1        5        3        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 14 33
  subtype2 37 77
  subtype3  6 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   33
  subtype2   37   77
  subtype3    6   15
     clus
vv    subtype1 subtype2 subtype3
  NO        14       37        6
  YES       33       77       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               22
  subtype2             0                              193
  subtype3             0                               37
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  21
  subtype2                                   0
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           16
  subtype2                                            1
  subtype3                                            0
D6V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    22      193       37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 21        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        16        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                         3
  subtype2                                4    13                        20
  subtype3                                2     1                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    53
  subtype2                                         2   130
  subtype3                                         0    26
D6V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        4        2
  ASIAN                                            6       13        1
  BLACK OR AFRICAN AMERICAN                        3       20        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        2        0
  WHITE                                           53      130       26
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
          cls
clus         0   1
  subtype1   6  38
  subtype2  16 108
  subtype3   2  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   38
  subtype2   16  108
  subtype3    2   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       16        2
  NOT HISPANIC OR LATINO       38      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  42  22
  subtype2 126  44
  subtype3  21  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   22
  subtype2  126   44
  subtype3   21   12
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       42      126       21
  WITH TUMOR       22       44       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  7 30 29  0  6
  subtype2 10 93 69  0 16
  subtype3  1 12 20  1  2
D6V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        7       10        1
  G2       30       93       12
  G3       29       69       20
  G4        0        0        1
  GX        6       16        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, continuous
D6V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           9
  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                  44
  subtype2                  85
  subtype3                  15
D6V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            9       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                                   44       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"
D6V18, continuous
D6V19, binary
          cls
clus        0  1
  subtype1  3  0
  subtype2 20  2
  subtype3  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2   20    2
  subtype3    6    1
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           3       20        6
  TREATMENT NOT COMPLETED        0        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V20, continuous
D6V21, continuous
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       9
  subtype2                                   5                      26
  subtype3                                   2                       5
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       7
  subtype3                       0                       1
D6V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        5        2
  OTHER LOCATION, SPECIFY                    9       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                                                                                19
  subtype2                                                                                61
  subtype3                                                                                 2
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           34
  subtype2                                                                                           72
  subtype3                                                                                           18
D6V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       34
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       72
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       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"
D6V28, binary
          cls
clus        0  1
  subtype1 23 21
  subtype2 39 50
  subtype3  9  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   21
  subtype2   39   50
  subtype3    9    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       39        9
  PRESENT       21       50        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V29, continuous
D6V30, continuous
D6V31, binary
          cls
clus        0  1
  subtype1  0 17
  subtype2 47 89
  subtype3  8 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   17
  subtype2   47   89
  subtype3    8   13
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       47        8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17       89       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          17         21
  subtype2            4          32         59
  subtype3            4           4          9
D6V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        7        4        4
  FORMER USER        17       32        4
  NEVER USED         21       59        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V34, continuous
D6V35, binary
          cls
clus        0  1
  subtype1 31  6
  subtype2 56 13
  subtype3 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    6
  subtype2   56   13
  subtype3   12    0
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        31       56       12
  PRESENT        6       13        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           3        22     1
  subtype2           4        67     0
  subtype3           0        13     1
D6V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        3        4        0
  CISPLATIN         22       67       13
  OTHER              1        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1       13        3 
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2"
D6V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        6        28        10
  subtype2       4        1         1         1       24        44        20
  subtype3       0        0         0         0        8         5         9
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         3          1          2         8         0
  subtype2        4         3          2          4        30         1
  subtype3        0         3          2          1         5         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          6         1         5
  subtype2          2         33         8         7
  subtype3          0          3         0         0
D6V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA          0        1        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          6       24        8
  STAGE IB1        28       44        5
  STAGE IB2        10       20        9
  STAGE II          1        4        0
  STAGE IIA         3        3        3
  STAGE IIA1        1        2        2
  STAGE IIA2        2        4        1
  STAGE IIB         8       30        5
  STAGE III         0        1        0
  STAGE IIIA        0        2        0
  STAGE IIIB        6       33        3
  STAGE IVA         1        8        0
  STAGE IVB         5        7        0
[1] 17  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 74 25
  subtype2 62 15
  subtype3 83 31
subtype1 subtype2 subtype3 
      99       77      114 
subtype1 subtype2 subtype3 
      25       15       31 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       17.52        82.85        31.40        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2M1 
       53.16        35.61        20.91        33.90        44.22        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-C5-A902 
       33.24        18.02        20.35         2.73        27.52         4.90 
TCGA-C5-A905 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WI 
      160.41         1.12        95.11        82.06        16.18         8.28 
TCGA-EA-A3QD TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       13.05        26.40        31.73        24.82        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IR TCGA-EK-A2R7 TCGA-EK-A2RA 
       25.91        27.22        24.00       113.16         0.36        40.96 
TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
       47.77         0.49        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        14.01        35.44         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        44.61 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MY-A5BD TCGA-MY-A5BE 
       20.91         0.30        13.35        19.56        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 
       18.64        22.62        69.50        10.03        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A952 TCGA-VS-A953 
       19.96        32.15        36.13        11.51        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD 
       56.35        55.50        51.32        48.39        28.50        24.30 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR 
        1.71        14.53        27.25        47.87        47.47        26.07 
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 
       17.75         4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1M5 TCGA-C5-A1MJ TCGA-C5-A1MP 
       17.82        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        63.98        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         0.30         7.46        27.29        27.25 
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         4.31 
TCGA-EK-A2RK TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3NI 
        0.43         0.76        20.35         7.92        16.11        20.98 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.48        16.14        28.31        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
       20.78        14.93       147.39       129.37        96.95        78.71 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3W TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       11.28         0.89        22.52        11.38        28.08        34.62 
TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A9UQ 
       16.41        93.99        12.16        31.27        40.87        41.52 
TCGA-VS-A9UT TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       15.85        18.25        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 
       14.73        87.75        55.63        69.96        95.67         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        40.87        37.35        33.30 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       25.02        36.89        26.01        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RD 
        6.64         1.51         0.39         0.43         0.59         0.10 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23L 
        0.53         0.10         0.03        15.22         8.32        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-GH-A9DA TCGA-IR-A3LK 
       19.04        31.36        26.14        10.55        17.75        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42        24.56        21.44        20.48        15.58 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3Y 
        8.28        21.11       209.59        12.49         0.82        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM TCGA-MY-A913 TCGA-Q1-A5R3 
       19.56         8.35         8.52        19.96        17.23        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.04        17.56        14.07        19.59        14.60        11.67 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QF 
       32.42        23.97        27.25        65.49        53.59        59.18 
TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A958 
       39.78        16.64         4.73        33.37        40.14        50.14 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI 
       50.47        43.40        29.95        27.12        46.92        45.11 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       15.42        26.01        67.59        19.13         0.69         0.16 

subtype1 subtype2 subtype3 
    0.30     0.13     0.03 
subtype1 subtype2 subtype3 
  160.41   210.67   209.59 
subtype1 subtype2 subtype3 
  24.300   20.980   24.265 
[1] "0.3 - 160.4 (24.3)" "0.1 - 210.7 (21.0)" "0.0 - 209.6 (24.3)"
D7V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 50 29 10  5
  subtype2 45 16  3  1
  subtype3 46 27  8  4
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       50       45       46
  T2       29       16       27
  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 46 19
  subtype2 41 22
  subtype3 48 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   19
  subtype2   41   22
  subtype3   48   19
   clus
vv  subtype1 subtype2 subtype3
  0       46       41       48
  1       19       22       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 38  6
  subtype2 35  1
  subtype3 43  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    6
  subtype2   35    1
  subtype3   43    3
   clus
vv  subtype1 subtype2 subtype3
  0       38       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"
D7V6, binary
          cls
clus        0  1
  subtype1 23 49
  subtype2 13 30
  subtype3 21 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   49
  subtype2   13   30
  subtype3   21   48
     clus
vv    subtype1 subtype2 subtype3
  NO        23       13       21
  YES       49       30       48
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               61
  subtype2             1                               70
  subtype3             0                              123
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  17
  subtype2                                   4
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           12
  subtype2                                            4
  subtype3                                            1
D7V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    61       70      123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 17        4        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        12        4        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                         9
  subtype2                                1     8                         7
  subtype3                                6     4                        14
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    68
  subtype2                                         0    55
  subtype3                                         2    88
D7V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        6
  ASIAN                                            8        8        4
  BLACK OR AFRICAN AMERICAN                        9        7       14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           68       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 53
  subtype2  5 50
  subtype3 12 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   53
  subtype2    5   50
  subtype3   12   67
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        5       12
  NOT HISPANIC OR LATINO       53       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 62 31
  subtype2 56 15
  subtype3 73 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   31
  subtype2   56   15
  subtype3   73   32
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       62       56       73
  WITH TUMOR       31       15       32
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  8 40 43  0 11
  subtype2  8 41 28  1  1
  subtype3  2 55 49  0 12
D7V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        8        8        2
  G2       40       41       55
  G3       43       28       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"
D7V15, continuous
D7V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          13
  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                  35
  subtype3                  50
D7V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           13        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       35       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"
D7V18, continuous
D7V19, 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"
D7V20, continuous
D7V21, continuous
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       9
  subtype2                                   2                      15
  subtype3                                   4                      16
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       5
  subtype3                       0                       3
D7V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        4
  OTHER LOCATION, SPECIFY                    9       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                                                                                26
  subtype3                                                                                32
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           44
  subtype2                                                                                           29
  subtype3                                                                                           52
D7V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       44
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       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"
D7V28, binary
          cls
clus        0  1
  subtype1 24 30
  subtype2 23 28
  subtype3 25 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   30
  subtype2   23   28
  subtype3   25   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        24       23       25
  PRESENT       30       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"
D7V29, continuous
D7V30, continuous
D7V31, binary
          cls
clus        0  1
  subtype1  6 29
  subtype2 19 32
  subtype3 30 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   29
  subtype2   19   32
  subtype3   30   59
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            6       19       30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       29       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"
D7V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            8          20         34
  subtype2            3          16         20
  subtype3            4          18         36
D7V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        8        3        4
  FORMER USER        20       16       18
  NEVER USED         34       20       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"
D7V34, continuous
D7V35, binary
          cls
clus        0  1
  subtype1 34  8
  subtype2 33  7
  subtype3 32  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    8
  subtype2   33    7
  subtype3   32    4
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        34       33       32
  PRESENT        8        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           3        36     0
  subtype2           1        19     0
  subtype3           3        49     2
D7V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        3        1        3
  CISPLATIN         36       19       49
  OTHER              0        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V37, continuous
[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"
D7V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       2        0         0         0        8        30        15
  subtype2       0        1         1         1        9        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        26         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
D7V39, 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        9       21
  STAGE IB1        30       28       20
  STAGE IB2        15       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       26
  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 44 15
  subtype2 75 21
  subtype3 53 16
  subtype4 15  7
  subtype5 32 12
subtype1 subtype2 subtype3 subtype4 subtype5 
      59       96       69       22       44 
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       21       16        7       12 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS 
       17.52        31.40        57.73        35.61         0.46        44.22 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT 
       38.43        33.24        17.85        20.35         2.73        20.81 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A439 
        1.12        95.11        82.06        16.18        17.52        31.73 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM 
       24.82        14.89        26.79        47.77         0.49         0.76 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J 
        7.92        14.70        15.55         1.22        16.11        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       35.44         1.12         9.44       137.16        66.81        96.95 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P 
       28.37        44.61        13.35        15.58        16.14        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       18.64        22.62        69.50        36.13        39.78        58.45 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
        1.71        14.53        47.87        41.52        26.07        15.85 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-VS-A9V5 
       67.20        18.84         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 
       17.82        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         0.30         7.46 
TCGA-EA-A5O9 TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PM 
       25.91        24.00        12.59       113.16         1.51         0.59 
TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EK-A3GN TCGA-EX-A69L 
        0.36        40.96         0.10         0.53         0.03        19.79 
TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A5XV 
        8.32        19.04        31.36        26.14        16.14        10.55 
TCGA-HG-A9SC TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 
       16.57        81.96        24.56        21.44        20.48         8.28 
TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Z 
       18.15        20.91         0.30         0.82        19.56        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R3 
        8.52        11.38        19.96        54.81        20.84        15.95 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-UC-A7PG TCGA-VS-A8EG TCGA-VS-A8EH 
       17.56        14.07         9.34        12.16        45.57        32.42 
TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A94Z TCGA-VS-A950 
       27.25        65.49        32.15        11.51        33.37        40.14 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UM TCGA-VS-A9UU 
       43.40        48.39        28.50        24.30        27.25        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-WL-A834 TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
        3.42        18.25        17.75        26.01         0.69         0.16 

$subtype3
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 
       49.48        23.67        68.84        36.56       177.04        67.46 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LY 
       46.32        38.99         2.43        40.93         3.58        78.35 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE 
       20.42       210.67       101.82       134.33       147.35       155.77 
TCGA-C5-A7XC TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.99        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS 
       55.63        69.96         8.75        28.90        16.83        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5ZD 
       40.87        37.35        31.53        31.36        13.05        27.29 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       27.25        13.48         0.36         1.45         0.13         4.31 
TCGA-EK-A2RK TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.43        20.35        20.98        28.31        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       129.37        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        28.08        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        53.59        31.27        40.87        18.25 
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        95.67        12.36 
TCGA-EA-A410 TCGA-EA-A5ZF TCGA-EK-A2PI TCGA-FU-A23L TCGA-FU-A3HZ TCGA-JW-A5VH 
       26.40        27.22        19.27        23.84        36.26         3.29 
TCGA-JX-A3Q0 TCGA-MA-AA41 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-VS-A8EC TCGA-VS-A94X 
      209.59         8.35         2.96         9.04        46.52        16.64 
TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UP TCGA-ZJ-A8QR 
       27.12        45.11        47.47        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        14.73 
TCGA-DS-A1OD TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 
      127.36         8.28        36.89        26.01        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-FU-A3TX 
        6.64         0.39         0.43         0.10        15.22         1.48 
TCGA-GH-A9DA TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU 
       17.75        78.71        27.42        15.58        21.11        11.28 
TCGA-LP-A4AX TCGA-MA-AA3Y TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB 
       12.49        17.82        17.23        14.60        11.67        10.03 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A9UB TCGA-VS-A9UH 
       23.97        19.96        59.18         4.73        29.95        46.92 
TCGA-VS-AA62 TCGA-ZJ-A8QQ 
       15.42        67.59 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.03     0.13     2.96     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  137.16   160.41   210.67   209.59   144.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
   18.84    20.91    31.36    26.76    17.92 
[1] "0.5 - 137.2 (18.8)" "0.0 - 160.4 (20.9)" "0.1 - 210.7 (31.4)"
[4] "3.0 - 209.6 (26.8)" "0.1 - 144.2 (17.9)"
D8V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 35 13  2  1
  subtype2 32 29 12  6
  subtype3 47 11  2  1
  subtype4  8  9  2  1
  subtype5 19 10  3  1
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       35       32       47        8       19
  T2       13       29       11        9       10
  T3        2       12        2        2        3
  T4        1        6        1        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus        0  1
  subtype1 32 10
  subtype2 33 22
  subtype3 38 20
  subtype4 11  2
  subtype5 21  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   10
  subtype2   33   22
  subtype3   38   20
  subtype4   11    2
  subtype5   21    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       32       33       38       11       21
  1       10       22       20        2        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 18  2
  subtype2 29  2
  subtype3 38  1
  subtype4 12  2
  subtype5 19  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    2
  subtype2   29    2
  subtype3   38    1
  subtype4   12    2
  subtype5   19    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       18       29       38       12       19
  1        2        2        1        2        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 11 28
  subtype2 18 50
  subtype3 14 19
  subtype4  7 10
  subtype5  7 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   28
  subtype2   18   50
  subtype3   14   19
  subtype4    7   10
  subtype5    7   20
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        11       18       14        7        7
  YES       28       50       19       10       20
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               13
  subtype2             1                               99
  subtype3             0                               74
  subtype4             0                               24
  subtype5             0                               44
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             1
  subtype3                                             0
  subtype4                                             1
  subtype5                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   1
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           16
  subtype2                                            0
  subtype3                                            0
  subtype4                                            1
  subtype5                                            0
D8V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    13       99       74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        16        0        0
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    24       44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         1        0
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         2
  subtype2                                3     5                        13
  subtype3                                1     6                         7
  subtype4                                1     2                         3
  subtype5                                3     2                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    45
  subtype2                                         0    66
  subtype3                                         0    51
  subtype4                                         1    17
  subtype5                                         1    32
D8V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        3        1        1
  ASIAN                                            5        5        6        2
  BLACK OR AFRICAN AMERICAN                        2       13        7        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           45       66       51       17
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 3
  ASIAN                                            2
  BLACK OR AFRICAN AMERICAN                        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           32
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus        0  1
  subtype1  4 31
  subtype2 10 52
  subtype3  3 50
  subtype4  3 16
  subtype5  4 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   31
  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       31       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 38 17
  subtype2 64 25
  subtype3 50 15
  subtype4 12  9
  subtype5 27 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   17
  subtype2   64   25
  subtype3   50   15
  subtype4   12    9
  subtype5   27   12
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       38       64       50       12       27
  WITH TUMOR       17       25       15        9       12
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 27 21  0  6
  subtype2  4 46 38  0  8
  subtype3  6 39 28  0  1
  subtype4  0 14  9  0  3
  subtype5  2 10 24  1  6
D8V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        6        4        6        0        2
  G2       27       46       39       14       10
  G3       21       38       28        9       24
  G4        0        0        0        0        1
  GX        6        8        1        3        6
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
D8V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           9
  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                  34
  subtype2                  45
  subtype3                  34
  subtype4                  14
  subtype5                  19
D8V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            9       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                                   34       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"
D8V18, continuous
D8V19, binary
          cls
clus       0 1
  subtype1 3 0
  subtype2 7 0
  subtype3 9 1
  subtype4 2 0
  subtype5 8 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    7    0
  subtype3    9    1
  subtype4    2    0
  subtype5    8    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  COMPLETED AS PLANNED           3        7        9        2        8
  TREATMENT NOT COMPLETED        0        0        1        0        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V20, continuous
D8V21, continuous
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   2
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       7
  subtype2                                   3                       8
  subtype3                                   3                      16
  subtype4                                   0                       2
  subtype5                                   2                       7
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       4
  subtype3                       0                       3
  subtype4                       0                       0
  subtype5                       0                       1
D8V26, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       16       23        2       10 
 [1] "subtype1" "subtype3" "subtype5" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype5" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype5" "subtype1" "subtype5" "subtype5"
[19] "subtype2" "subtype1" "subtype5" "subtype3" "subtype3" "subtype3"
[25] "subtype5" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[31] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype5" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[49] "subtype3" "subtype5" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype5" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        2        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0        3        3        2
  OTHER LOCATION, SPECIFY                    7        8       16        7
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        4        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                                                                                16
  subtype2                                                                                29
  subtype3                                                                                30
  subtype4                                                                                 5
  subtype5                                                                                 4
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           30
  subtype2                                                                                           37
  subtype3                                                                                           23
  subtype4                                                                                            9
  subtype5                                                                                           26
D8V27, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       23
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        9
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       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"
D8V28, binary
          cls
clus        0  1
  subtype1 21 16
  subtype2 17 24
  subtype3 19 29
  subtype4  5  3
  subtype5 10  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   16
  subtype2   17   24
  subtype3   19   29
  subtype4    5    3
  subtype5   10    8
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        21       17       19        5       10
  PRESENT       16       24       29        3        8
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V29, continuous
D8V30, continuous
D8V31, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2 21 46
  subtype3 20 34
  subtype4  4 12
  subtype5 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2   21   46
  subtype3   20   34
  subtype4    4   12
  subtype5   10   17
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       21       20        4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       11       46       34       12
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA           10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       17
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          14         18
  subtype2            4          17         33
  subtype3            1          14         19
  subtype4            0           5          7
  subtype5            4           4         13
D8V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        6        4        1        0        4
  FORMER USER        14       17       14        5        4
  NEVER USED         18       33       19        7       13
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V34, continuous
D8V35, binary
          cls
clus        0  1
  subtype1 27  4
  subtype2 22  5
  subtype3 32  8
  subtype4  5  2
  subtype5 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    4
  subtype2   22    5
  subtype3   32    8
  subtype4    5    2
  subtype5   13    0
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        27       22       32        5       13
  PRESENT        4        5        8        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           2        18     1
  subtype2           2        36     0
  subtype3           2        20     0
  subtype4           1         8     0
  subtype5           0        22     1
D8V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        2        2        2        1        0
  CISPLATIN         18       36       20        8       22
  OTHER              1        0        0        0        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V37, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype5 
       1        5        8        3 
 [1] "subtype5" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [7] "subtype5" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype5" "subtype3"
D8V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        5        26         9
  subtype2       2        0         0         0        7        17        12
  subtype3       0        1         1         1       13        25         8
  subtype4       2        0         0         0        6         1         2
  subtype5       0        0         0         0        7         9         8
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         2          1          0         5         0
  subtype2        3         1          0          3        18         0
  subtype3        1         2          1          1         5         0
  subtype4        0         1          1          2         5         1
  subtype5        0         3          2          1        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IVA STAGE IVB
  subtype1          0          6         1         3
  subtype2          3         19         5         6
  subtype3          0         11         2         1
  subtype4          0          3         0         2
  subtype5          0          3         1         0
D8V39, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        2        0        2        0
  STAGE IA          0        0        1        0        0
  STAGE IA1         0        0        1        0        0
  STAGE IA2         0        0        1        0        0
  STAGE IB          5        7       13        6        7
  STAGE IB1        26       17       25        1        9
  STAGE IB2         9       12        8        2        8
  STAGE II          1        3        1        0        0
  STAGE IIA         2        1        2        1        3
  STAGE IIA1        1        0        1        1        2
  STAGE IIA2        0        3        1        2        1
  STAGE IIB         5       18        5        5       11
  STAGE III         0        0        0        1        0
  STAGE IIIA        0        3        0        0        0
  STAGE IIIB        6       19       11        3        3
  STAGE IVA         1        5        2        0        1
  STAGE IVB         3        6        1        2        0
[1] 17  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 98 25
  subtype2 57 17
  subtype3 57 26
subtype1 subtype2 subtype3 
     123       74       83 
subtype1 subtype2 subtype3 
      25       17       26 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2M1 TCGA-C5-A2M2 
       17.52        31.40        35.01        57.73        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7UC 
       52.01        18.02       210.67       154.32        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
      131.11        13.61         2.73         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52         4.90       160.41        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       82.06        16.18         8.28        36.89        26.40        26.01 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IR 
       24.82        14.89        26.79        27.22        12.59       113.16 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GN 
        1.51         0.39         0.36        47.77         0.49         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        19.04        36.26        14.01 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LI TCGA-JW-A5VG 
       10.55         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        44.61        20.91        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        19.56        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        17.23         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        18.64 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       22.62        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8EK TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       19.96        27.25        53.59        36.13        59.18        39.78 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       40.14        58.45        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UJ 
       43.40        28.50        29.95        27.12        24.30         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UV 
       14.53        27.25        47.87        47.47        26.07         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 
       18.25        67.20        18.84         5.16        17.75         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 
       17.82        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        31.73         0.30         7.46 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2PI 
       27.29        27.25        13.48         0.36        26.27        19.27 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RK TCGA-EK-A3GM 
        0.59         1.45         0.13         4.31         0.43         0.76 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB 
        7.92        15.22        16.11        20.98         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       28.31        35.44        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-LP-A4AW 
       14.93       147.39        66.81       129.37        96.95         0.89 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QC 
       28.08        19.96        16.41        93.99        23.97        11.51 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9V2 TCGA-WL-A834 
       31.27        40.87        41.52        15.85        18.25        26.01 
TCGA-XS-A8TJ TCGA-ZX-AA5X 
       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        63.98 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA 
       87.75        55.63        69.96        95.67         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        40.87        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        24.00        60.72         6.64 
TCGA-EK-A2PL TCGA-EK-A2RA TCGA-EK-A3GJ TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3HY 
        0.43        40.96         0.10         1.22        23.84        31.36 
TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JX-A3PZ 
       26.14        17.75        78.71        29.85        36.36        21.11 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-Q1-A6DT TCGA-Q1-A73O 
       22.52        17.82         8.35         8.52         9.04        14.07 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A94X 
       19.59        14.60        11.67        65.49        32.15        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UH TCGA-VS-A9UI 
        4.73        33.37        56.35        48.39        46.92        45.11 
TCGA-VS-A9UU TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       14.53        15.42        67.59        19.13         0.16 

subtype1 subtype2 subtype3 
    0.03     0.13     0.10 
subtype1 subtype2 subtype3 
  210.67   147.39   177.04 
subtype1 subtype2 subtype3 
  20.480   20.795   33.300 
[1] "0.0 - 210.7 (20.5)" "0.1 - 147.4 (20.8)" "0.1 - 177.0 (33.3)"
D9V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 53 33 12  6
  subtype2 39 15  3  1
  subtype3 44 20  4  2
D9V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       53       39       44
  T2       33       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 52 16
  subtype2 41 17
  subtype3 37 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   16
  subtype2   41   17
  subtype3   37   24
   clus
vv  subtype1 subtype2 subtype3
  0       52       41       37
  1       16       17       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 40  7
  subtype2 32  1
  subtype3 40  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    7
  subtype2   32    1
  subtype3   40    1
   clus
vv  subtype1 subtype2 subtype3
  0       40       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"
D9V6, binary
          cls
clus        0  1
  subtype1 31 65
  subtype2 11 27
  subtype3 12 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   65
  subtype2   11   27
  subtype3   12   31
     clus
vv    subtype1 subtype2 subtype3
  NO        31       11       12
  YES       65       27       31
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             5                               90
  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                                   6
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                           13
  subtype2                                            4
  subtype3                                            0
D9V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        5        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    90       65       87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        6        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        13        4        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                5     9                        15
  subtype2                                1     7                         3
  subtype3                                1     3                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    82
  subtype2                                         0    58
  subtype3                                         2    65
D9V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 5        1        1
  ASIAN                                            9        7        3
  BLACK OR AFRICAN AMERICAN                       15        3        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        2
  WHITE                                           82       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 64
  subtype2  3 48
  subtype3  7 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   64
  subtype2    3   48
  subtype3    7   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        3        7
  NOT HISPANIC OR LATINO       64       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 77 36
  subtype2 53 16
  subtype3 56 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   36
  subtype2   53   16
  subtype3   56   22
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       77       53       56
  WITH TUMOR       36       16       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"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 47 60  0 13
  subtype2  8 42 25  0  2
  subtype3  2 39 33  1  8
D9V14, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        8        2
  G2       47       42       39
  G3       60       25       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"
D9V15, continuous
D9V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          17
  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                  35
  subtype3                  37
D9V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           17        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       35       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"
D9V18, continuous
D9V19, 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"
D9V20, continuous
D9V21, continuous
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       9
  subtype2                                   2                      11
  subtype3                                   4                      19
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       4
  subtype3                       0                       4
D9V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        2        4
  OTHER LOCATION, SPECIFY                    9       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                                                                                23
  subtype3                                                                                25
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           52
  subtype2                                                                                           30
  subtype3                                                                                           38
D9V27, 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)       52
                                                                                              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)                  23
  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"
D9V28, binary
          cls
clus        0  1
  subtype1 23 24
  subtype2 24 23
  subtype3 22 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   24
  subtype2   24   23
  subtype3   22   27
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       24       22
  PRESENT       24       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"
D9V29, continuous
D9V30, continuous
D9V31, binary
          cls
clus        0  1
  subtype1 10 45
  subtype2 18 30
  subtype3 24 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   45
  subtype2   18   30
  subtype3   24   39
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           10       18       24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       45       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"
D9V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          22         44
  subtype2            4          16         18
  subtype3            5          16         23
D9V33, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        6        4        5
  FORMER USER        22       16       16
  NEVER USED         44       18       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"
D9V34, continuous
D9V35, binary
          cls
clus        0  1
  subtype1 29  5
  subtype2 30  5
  subtype3 36  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    5
  subtype2   30    5
  subtype3   36    9
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        29       30       36
  PRESENT        5        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           4        52     1
  subtype2           0        17     1
  subtype3           3        33     0
D9V36, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        4        0        3
  CISPLATIN         52       17       33
  OTHER              1        1        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"
D9V37, continuous
D9V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       3        0         0        9        35        18        2
  subtype2       0        1         1        6        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        19          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
D9V39, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        2
  STAGE IA          0        1        0
  STAGE IA2         0        1        0
  STAGE IB          9        6       22
  STAGE IB1        35       24       17
  STAGE IB2        18       12        7
  STAGE II          2        2        1
  STAGE IIA         4        3        1
  STAGE IIA1        0        3        2
  STAGE IIA2        4        2        1
  STAGE IIB        19        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  47  15
  subtype2  36  10
  subtype3  19  12
  subtype4 110  31
subtype1 subtype2 subtype3 subtype4 
      62       46       31      141 
subtype1 subtype2 subtype3 subtype4 
      15       10       12       31 
$subtype1
TCGA-2W-A8YY TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       17.52        57.73         0.46        44.22        38.43        33.24 
TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ 
       17.85        20.35         2.73        20.81         1.12        95.11 
TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA 
       82.06        16.18        17.52        26.40        31.73        24.82 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM 
       14.89        27.22         0.36        47.77         0.49         0.76 
TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        7.92        16.11        36.26        14.01        35.44         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        44.61        13.35        54.81         2.96        15.58 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA 
       16.14        15.88        18.64        69.50        19.96        36.13 
TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP 
       39.78        58.45         1.71        14.53        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       41.52        26.07        15.85        67.20        18.84         5.16 
TCGA-VS-A9V4 TCGA-VS-A9V5 
        4.34        16.24 

$subtype2
TCGA-4J-AA1J TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
       17.82        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         0.30         7.46 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PI TCGA-EK-A2PM 
       27.29        27.25        13.48         0.36        19.27         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RK TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HG-A9SC 
        0.13         4.31         0.43        20.98        25.41        16.57 
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 
       28.08        19.96        16.41        93.99        23.97        32.15 
TCGA-VS-A8QM TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZX-AA5X 
       31.27        18.25        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        55.63 
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        40.87         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        14.73        63.98 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ 
       69.96        95.67         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        36.89        26.01        26.79 
TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2IR 
       24.00        12.59        60.72        26.27         6.64       113.16 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A3GJ 
        1.51         0.39         0.43         1.45        40.96         0.10 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG 
        0.03        15.22        19.79         8.32        15.55        19.04 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A5XV 
       31.36        26.14         1.48        16.14        28.31        10.55 
TCGA-GH-A9DA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       17.75       129.37        78.71        29.85        36.36        27.42 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        20.48        15.58         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       21.11        20.91        11.28        12.49         0.30         0.82 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       19.56        17.82        19.56         8.35         8.52        11.38 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       35.05        20.84        17.23        15.95         9.04        17.56 
TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       14.07         9.34        22.62        19.59        14.60        11.67 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EK TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        27.25        65.49 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       53.59        11.51        59.18        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       33.37        40.14        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9UV 
       24.30        46.92        45.11        27.25        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       18.25        17.75        15.42        26.01        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        0.69         1.41         0.16 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.13     1.22     0.03 
subtype1 subtype2 subtype3 subtype4 
  137.16   147.39   177.04   210.67 
subtype1 subtype2 subtype3 subtype4 
  20.155   21.325   36.760   21.440 
[1] "0.4 - 137.2 (20.2)" "0.1 - 147.4 (21.3)" "1.2 - 177.0 (36.8)"
[4] "0.0 - 210.7 (21.4)"
D10V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 33 19  2  2
  subtype2 26  8  3  1
  subtype3 18  5  1  0
  subtype4 59 36 13  6
D10V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       33       26       18       59
  T2       19        8        5       36
  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 35  9
  subtype2 25 11
  subtype3 13 11
  subtype4 57 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    9
  subtype2   25   11
  subtype3   13   11
  subtype4   57   26
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       35       25       13       57
  1        9       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 22  4
  subtype2 24  1
  subtype3 15  0
  subtype4 51  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    4
  subtype2   24    1
  subtype3   15    0
  subtype4   51    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       22       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"
D10V6, binary
          cls
clus        0  1
  subtype1 14 29
  subtype2  8 18
  subtype3  4  2
  subtype4 28 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   29
  subtype2    8   18
  subtype3    4    2
  subtype4   28   74
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        14        8        4       28
  YES       29       18        2       74
[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             4                               16
  subtype2             1                               49
  subtype3             0                               30
  subtype4             1                              147
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             0
  subtype3                                             0
  subtype4                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  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                                           17
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
D10V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    16       49       30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE        17        0        0
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        1
  CERVICAL SQUAMOUS CELL CARCINOMA                   147
  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"
D10V8, continuous
D10V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                         3
  subtype2                                1     5                         2
  subtype3                                0     2                         3
  subtype4                                5     6                        19
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    45
  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                                            6        5        2        6
  BLACK OR AFRICAN AMERICAN                        3        2        3       19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        2
  WHITE                                           45       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 33
  subtype2  3 31
  subtype3  1 22
  subtype4 14 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   33
  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       33       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 39 19
  subtype2 33 10
  subtype3 19 11
  subtype4 95 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   19
  subtype2   33   10
  subtype3   19   11
  subtype4   95   34
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       39       33       19       95
  WITH TUMOR       19       10       11       34
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 28 24  0  6
  subtype2  5 28 14  0  2
  subtype3  0 17 14  0  0
  subtype4  5 55 66  1 15
D10V14, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        6        5        0        5
  G2       28       28       17       55
  G3       24       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"
D10V15, continuous
D10V16, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           8
  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                  38
  subtype2                  22
  subtype3                  14
  subtype4                  69
D10V17, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            8        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                                   38       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"
D10V18, continuous
D10V19, 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"
D10V20, continuous
D10V21, continuous
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       7
  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
D10V26, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        2        3
  OTHER LOCATION, SPECIFY                    7        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                                                                                17
  subtype2                                                                                15
  subtype3                                                                                12
  subtype4                                                                                34
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           30
  subtype2                                                                                           18
  subtype3                                                                                           14
  subtype4                                                                                           58
D10V27, 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)                  17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              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"
D10V28, binary
          cls
clus        0  1
  subtype1 21 16
  subtype2 14 15
  subtype3  6 18
  subtype4 28 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   16
  subtype2   14   15
  subtype3    6   18
  subtype4   28   25
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        21       14        6       28
  PRESENT       16       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"
D10V29, continuous
D10V30, continuous
D10V31, binary
          cls
clus        0  1
  subtype1  0 12
  subtype2 14 21
  subtype3  9 12
  subtype4 29 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   12
  subtype2   14   21
  subtype3    9   12
  subtype4   29   69
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       14        9       29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       12       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"
D10V32, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            7          14         21
  subtype2            0          10         11
  subtype3            0           5         10
  subtype4            8          25         43
D10V33, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        7        0        0        8
  FORMER USER        14       10        5       25
  NEVER USED         21       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"
D10V34, continuous
D10V35, binary
          cls
clus        0  1
  subtype1 27  5
  subtype2 18  4
  subtype3 17  6
  subtype4 33  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    5
  subtype2   18    4
  subtype3   17    6
  subtype4   33    4
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        27       18       17       33
  PRESENT        5        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           3        19     1
  subtype2           0        12     0
  subtype3           3         9     0
  subtype4           1        62     1
D10V36, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  CARBOPLATIN        3        0        3        1
  CISPLATIN         19       12        9       62
  OTHER              1        0        0        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"
D10V37, 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"
D10V38, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       1        0         0        6        23        10        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        27          3         23
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         4
  subtype2         2         1
  subtype3         0         0
  subtype4         5         6
D10V39, 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          6        4       12       15
  STAGE IB1        23       17        5       31
  STAGE IB2        10        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       27
  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"
