[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPAPOBEC"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "APOBEC"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/22489370/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/CESC-TP/22522824/APOBEC_clinical_corr_input_22539499/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=307, in cluster file=194, common to both=194
[1]   2 194
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  46   74   74 
   0 HIGH  LOW 
  46   74   74 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           141              7             46 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           141              7             46 
[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 194 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=41,	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=139,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'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=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	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=66,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'AGEBEGANSMOKINGINYEARS':	nDistinctValues=22,	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=14,	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=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 29:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	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=7,	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"
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "6"                                                                                                                                
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NO PELVIC SPREAD PELVIC SPREAD
freq.values   "1"                       "1"              "1"          
freq.contrast "6"                       "6"              "6"          
both >= 3     "FALSE"                   "FALSE"          "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "6"                                                                         
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "6"                                                                                                                                       
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "6"                                                                      
both >= 3     "FALSE"                                                                  
Variable 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=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'LYMPH_NODES_EXAMINED':	nDistinctValues=47,	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=31,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'CAUSE_OF_DEATH':	nDistinctValues=2,	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"
              LUNG CANCER RENAL FAILURE
freq.values   "1"         "1"          
freq.contrast "1"         "1"          
both >= 3     "FALSE"     "FALSE"      
Variable 48:'AGE_AT_DIAGNOSIS':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 194 columns, 1 survival variables, and 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=57, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
104  40   3   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  104    40     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
104  40   3   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  104    40     5 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=66, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=18, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=TRUE
AGEBEGANSMOKINGINYEARS, nv=22, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PREGNANCY_SPONTANEOUS_ABORTION_COUNT, nv=4, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, 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=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=47, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=31, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=10, binary=FALSE, numeric=TRUE
AGE_AT_DIAGNOSIS, nv=57, binary=FALSE, numeric=TRUE
CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2   0  1
  0    36 10
  HIGH 60 12
  LOW  54 20
   0 HIGH  LOW 
  46   72   74 
   0 HIGH  LOW 
  10   12   20 
$`0`
TCGA-EX-A449 TCGA-EX-A69M TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV 
       14.70         8.32        67.46        57.73        73.18        73.45 
TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CM TCGA-DG-A2KJ TCGA-DS-A1OA 
       78.35        33.24       210.67        20.35        95.11        28.90 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 TCGA-EA-A4BA 
       22.98        16.18         8.28        40.87        26.40        24.82 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2PK TCGA-EK-A2R9 TCGA-EK-A2RE 
       14.89        25.91        27.29         0.39         0.13         1.87 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
       47.77         1.64        20.35        16.11        36.26        26.14 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
       35.44        25.41        21.67        20.78         9.44       147.39 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
       27.42         3.29        20.48        28.37        44.61        20.91 
TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       16.14        18.64        22.62        14.60 

$HIGH
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LX 
       31.40        46.32        38.99         2.43        40.93        83.05 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7UH TCGA-DG-A2KK 
      100.14        52.01        18.02        15.48       131.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        63.98        58.88        36.76       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3Y4 
       16.83        17.52        31.36        33.30        13.05        36.89 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       31.73        26.01        60.72         6.64         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.89         1.45        40.96         4.24         0.07 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-FU-A23K 
        1.74         0.43         2.33         0.10         0.49        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
       23.84        19.04        31.36        28.31        14.01        10.55 
TCGA-IR-A3LA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      137.16        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y 
       21.44        15.58       209.59         0.30        13.35        28.08 
TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-Q1-A73P TCGA-UC-A7PF 
       54.81        16.41         9.04        14.07        15.88        93.99 

$LOW
TCGA-EK-A2GZ TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       12.59         1.48        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       68.84        18.74         5.46        30.21        35.01        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS 
       35.61         0.46        20.91         3.58        33.90        44.22 
TCGA-C5-A2M1 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       38.43        17.85        20.42       154.32       101.82       134.33 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DR-A0ZL 
      147.35        17.19       155.77         9.34         1.12        87.75 
TCGA-DS-A0VL TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3QE TCGA-EA-A411 
       55.63        39.55        37.35        30.90        25.02        24.56 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.13         7.46        26.79        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2RB TCGA-EK-A2RO TCGA-EK-A3GN 
       13.48        26.27        19.27         0.30         0.07         0.89 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A770 
        7.92        15.22        19.79        20.98        16.14         1.12 
TCGA-HM-A4S6 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A852 TCGA-JX-A3PZ 
       14.93        66.81       129.37        24.56         8.28        21.11 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MY-A5BE 
       11.28         0.89        12.49         0.82        34.62        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-R2-A69V 
       20.84        15.58        15.95        17.56         9.34        19.59 
TCGA-UC-A7PD TCGA-WL-A834 
       11.67        26.01 

   0 HIGH  LOW 
0.13 0.07 0.07 
     0   HIGH    LOW 
210.67 209.59 155.77 
     0   HIGH    LOW 
23.900 29.080 20.875 
[1] "0.1 - 210.7 (23.9)" "0.1 - 209.6 (29.1)" "0.1 - 155.8 (20.9)"
D1V2, continuous
      vv
clus   T1 T2 T3+T4
  0    28 10     2
  HIGH 35 17     1
  LOW  41 13     2
D1V3, multiclass
       clus
vv       0 HIGH LOW
  T1    28   35  41
  T2    10   17  13
  T3+T4  2    1   2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
      cls
clus    0  1
  0    24 11
  HIGH 34 17
  LOW  37 16
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      24   11
  HIGH   34   17
  LOW    37   16
   clus
vv   0 HIGH LOW
  0 24   34  37
  1 11   17  16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
      cls
clus    0  1
  0    19  3
  HIGH 25  1
  LOW  35  0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      19    3
  HIGH   25    1
  LOW    35    0
   clus
vv   0 HIGH LOW
  0 19   25  35
  1  3    1   0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus    0  1
  0    12 13
  HIGH 10 22
  LOW  18 17
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      12   13
  HIGH   10   22
  LOW    18   17
     clus
vv     0 HIGH LOW
  NO  12   10  18
  YES 13   22  17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  0                3                               30
  HIGH             0                               64
  LOW              1                               64
      vv
clus   ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  0                                                1
  HIGH                                             2
  LOW                                              2
      vv
clus   ENDOCERVICAL TYPE OF ADENOCARCINOMA
  0                                     10
  HIGH                                   6
  LOW                                    5
      vv
clus   ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  0                                            1
  HIGH                                         1
  LOW                                          0
      vv
clus   MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  0                                               1
  HIGH                                            1
  LOW                                             2
D1V7, multiclass
                                               clus
vv                                               0 HIGH LOW
  ADENOSQUAMOUS                                  3    0   1
  CERVICAL SQUAMOUS CELL CARCINOMA              30   64  64
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE  1    2   2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA           10    6   5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX      1    1   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE   1    1   2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  0                                   2     4                         6
  HIGH                                3     4                         5
  LOW                                 3    11                         5
      vv
clus   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  0                                            0    31
  HIGH                                         1    54
  LOW                                          0    53
D1V10, multiclass
                                           clus
vv                                           0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE           2    3   3
  ASIAN                                      4    4  11
  BLACK OR AFRICAN AMERICAN                  6    5   5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER  0    1   0
  WHITE                                     31   54  53
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
      cls
clus    0  1
  0     5 36
  HIGH  6 44
  LOW   3 55
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   36
  HIGH    6   44
  LOW     3   55
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      5    6   3
  NOT HISPANIC OR LATINO 36   44  55
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
D1V13, binary
      cls
clus    0  1
  0    35 10
  HIGH 54 14
  LOW  50 21
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      35   10
  HIGH   54   14
  LOW    50   21
            clus
vv            0 HIGH LOW
  TUMOR FREE 35   54  50
  WITH TUMOR 10   14  21
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   G1 G2 G3 G4 GX
  0     2 20 21  0  3
  HIGH  6 31 33  1  2
  LOW   6 37 28  0  3
D1V14, multiclass
    clus
vv    0 HIGH LOW
  G1  2    6   6
  G2 20   31  37
  G3 21   33  28
  G4  0    1   0
  GX  3    2   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"
D1V15, continuous
D1V16, continuous
D1V17, continuous
D1V18, continuous
D1V19, binary
      cls
clus    0  1
  0     5  0
  HIGH 10  2
  LOW  11  1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5    0
  HIGH   10    2
  LOW    11    1
                         clus
vv                         0 HIGH LOW
  COMPLETED AS PLANNED     5   10  11
  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"
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
      vv
clus   MACROSCOPIC PARAMETRIAL INVOLVEMENT MICROSCOPIC PARAMETRIAL INVOLVEMENT
  0                                      1                                   1
  HIGH                                   0                                   2
  LOW                                    0                                   4
      vv
clus   OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  0                          7                       0                       1
  HIGH                       9                       0                       7
  LOW                       14                       1                       0
D1V26, multiclass
                                     clus
vv                                     0 HIGH LOW
  MACROSCOPIC PARAMETRIAL INVOLVEMENT  1    0   0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT  1    2   4
  OTHER LOCATION, SPECIFY              7    9  14
  POSITIVE BLADDER MARGIN              0    0   1
  POSITIVE VAGINAL MARGIN              1    7   0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  0                                                2
  HIGH                                             0
  LOW                                              1
      vv
clus   PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  0                                                 0
  HIGH                                              2
  LOW                                               8
      vv
clus   POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  0                                                                                    9
  HIGH                                                                                31
  LOW                                                                                 20
      vv
clus   PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  0                                                                                              29
  HIGH                                                                                           28
  LOW                                                                                            31
D1V27, multiclass
                                                                                              clus
vv                                                                                              0
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                0
  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) 29
                                                                                              clus
vv                                                                                             HIGH
  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)              31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)   28
                                                                                              clus
vv                                                                                             LOW
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                  1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                 8
  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)  31
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V28, binary
      cls
clus    0  1
  0    17 16
  HIGH 20 26
  LOW  26 25
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      17   16
  HIGH   20   26
  LOW    26   25
         clus
vv         0 HIGH LOW
  ABSENT  17   20  26
  PRESENT 16   26  25
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V29, continuous
D1V30, continuous
D1V31, binary
      cls
clus    0  1
  0     5 24
  HIGH 20 28
  LOW  14 34
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   24
  HIGH   20   28
  LOW    14   34
                                          clus
vv                                          0 HIGH LOW
  KERATINIZING SQUAMOUS CELL CARCINOMA      5   20  14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 24   28  34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V32, continuous
      vv
clus   CURRENT USER FORMER USER NEVER USED
  0               2          11         17
  HIGH            2          18         14
  LOW             4          14         15
D1V33, multiclass
              clus
vv              0 HIGH LOW
  CURRENT USER  2    2   4
  FORMER USER  11   18  14
  NEVER USED   17   14  15
[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
  0    23  5
  HIGH 29  7
  LOW  36  4
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23    5
  HIGH   29    7
  LOW    36    4
         clus
vv         0 HIGH LOW
  ABSENT  23   29  36
  PRESENT  5    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
  0              3        14     0
  HIGH           1        21     0
  LOW            0        18     1
D1V36, multiclass
             clus
vv             0 HIGH LOW
  CARBOPLATIN  3    1   0
  CISPLATIN   14   21  18
  OTHER        0    0   1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
[1] "Remove cluster labels:" "0"                     
clus
   0 HIGH  LOW 
   2    3    5 
TCGA-C5-A1BN TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-EK-A2RO 
       "LOW"       "HIGH"        "LOW"       "HIGH"        "LOW"        "LOW" 
TCGA-JW-A852 TCGA-MU-A51Y 
       "LOW"       "HIGH" 
D1V38, continuous
      vv
clus   STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  0          1        0         0         0        8        12        10
  HIGH       1        0         0         1       11        18         7
  LOW        2        1         1         0        9        23        12
      vv
clus   STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III STAGE IIIB
  0           0         2          0          4         3         0          3
  HIGH        2         2          4          1         7         1         16
  LOW         2         2          1          2         4         0         10
      vv
clus   STAGE IVA STAGE IVB
  0            0         3
  HIGH         0         1
  LOW          2         1
D1V39, multiclass
            clus
vv            0 HIGH LOW
  STAGE I     1    1   2
  STAGE IA    0    0   1
  STAGE IA1   0    0   1
  STAGE IA2   0    1   0
  STAGE IB    8   11   9
  STAGE IB1  12   18  23
  STAGE IB2  10    7  12
  STAGE II    0    2   2
  STAGE IIA   2    2   2
  STAGE IIA1  0    4   1
  STAGE IIA2  4    1   2
  STAGE IIB   3    7   4
  STAGE III   0    1   0
  STAGE IIIB  3   16  10
  STAGE IVA   0    0   2
  STAGE IVB   3    1   1
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH 108  31
  FC.LOW.ENRICH    6   1
  FC.NO.ENRICH    36  10
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           139              7             46 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            31              1             10 
$FC.HIGH.ENRICH
TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
        1.48        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        19.86        31.40        46.32        30.21        35.01 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ 
       40.93         3.58        33.90        44.22        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
       38.43        52.01        18.02        17.85        20.42       154.32 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
      134.33        15.48       147.35        17.19       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH 
       36.76        55.63       117.99       118.65        16.83        17.52 
TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
       39.55        30.90        31.36        33.30        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E 
       36.89        24.56        31.73        26.01        12.13         7.46 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        27.22        24.00        13.48        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ 
        1.45        40.96         0.30         4.24         0.07         1.74 
TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        15.22        19.79        12.23        23.84        19.04 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
       31.36        20.98        16.14        28.31        14.01        10.55 
TCGA-FU-A770 TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        1.12        14.93       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ 
       78.71        81.96        29.85        36.36        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AX 
       15.58         8.28        21.11       209.59        11.28        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
        0.30         0.82        13.35        28.08        34.62        54.81 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       20.84        15.58        16.41        15.95         9.04        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
       14.07        15.88         9.34        19.59        11.67        93.99 
TCGA-WL-A834 
       26.01 

$FC.LOW.ENRICH
TCGA-EK-A2GZ TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-EA-A3HQ TCGA-EA-A5FO TCGA-LP-A4AW 
       12.59       101.82       155.77        37.35        26.79         0.89 
TCGA-MY-A5BE 
       35.05 

$FC.NO.ENRICH
TCGA-EX-A449 TCGA-EX-A69M TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV 
       14.70         8.32        67.46        57.73        73.18        73.45 
TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CM TCGA-DG-A2KJ TCGA-DS-A1OA 
       78.35        33.24       210.67        20.35        95.11        28.90 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 TCGA-EA-A4BA 
       22.98        16.18         8.28        40.87        26.40        24.82 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2PK TCGA-EK-A2R9 TCGA-EK-A2RE 
       14.89        25.91        27.29         0.39         0.13         1.87 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
       47.77         1.64        20.35        16.11        36.26        26.14 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
       35.44        25.41        21.67        20.78         9.44       147.39 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
       27.42         3.29        20.48        28.37        44.61        20.91 
TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       16.14        18.64        22.62        14.60 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.07           0.89           0.13 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        209.59         155.77         210.67 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         21.44          35.05          23.90 
[1] "0.1 - 209.6 (21.4)" "0.9 - 155.8 (35.0)" "0.1 - 210.7 (23.9)"
D2V2, continuous
                vv
clus             T1 T2 T3+T4
  FC.HIGH.ENRICH 73 28     3
  FC.LOW.ENRICH   3  2     0
  FC.NO.ENRICH   28 10     2
D2V3, multiclass
       clus
vv      FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T1                73             3           28
  T2                28             2           10
  T3+T4              3             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"
D2V4, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 67 32
  FC.LOW.ENRICH   4  1
  FC.NO.ENRICH   24 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   67   32
  FC.LOW.ENRICH     4    1
  FC.NO.ENRICH     24   11
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0             67             4           24
  1             32             1           11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 57  1
  FC.LOW.ENRICH   3  0
  FC.NO.ENRICH   19  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   57    1
  FC.LOW.ENRICH     3    0
  FC.NO.ENRICH     19    3
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0             57             3           19
  1              1             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"
D2V6, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 26 36
  FC.LOW.ENRICH   2  3
  FC.NO.ENRICH   12 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   26   36
  FC.LOW.ENRICH     2    3
  FC.NO.ENRICH     12   13
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO              26             2           12
  YES             36             3           13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  FC.HIGH.ENRICH             1                              121
  FC.LOW.ENRICH              0                                7
  FC.NO.ENRICH               3                               30
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  FC.HIGH.ENRICH                                             4
  FC.LOW.ENRICH                                              0
  FC.NO.ENRICH                                               1
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  FC.HIGH.ENRICH                                  11
  FC.LOW.ENRICH                                    0
  FC.NO.ENRICH                                    10
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  FC.HIGH.ENRICH                                         1
  FC.LOW.ENRICH                                          0
  FC.NO.ENRICH                                           1
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  FC.HIGH.ENRICH                                            3
  FC.LOW.ENRICH                                             0
  FC.NO.ENRICH                                              1
D2V7, multiclass
                                               clus
vv                                              FC.HIGH.ENRICH FC.LOW.ENRICH
  ADENOSQUAMOUS                                              1             0
  CERVICAL SQUAMOUS CELL CARCINOMA                         121             7
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              4             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       11             0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  1             0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               3             0
                                               clus
vv                                              FC.NO.ENRICH
  ADENOSQUAMOUS                                            3
  CERVICAL SQUAMOUS CELL CARCINOMA                        30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             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"
D2V8, continuous
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            41              2             14 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CK     TCGA-C5-A7CL 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DR-A0ZM 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556     TCGA-EX-A1H5 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" 
    TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
D2V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.ENRICH                                6    14
  FC.LOW.ENRICH                                 0     1
  FC.NO.ENRICH                                  2     4
                vv
clus             BLACK OR AFRICAN AMERICAN
  FC.HIGH.ENRICH                         8
  FC.LOW.ENRICH                          2
  FC.NO.ENRICH                           6
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FC.HIGH.ENRICH                                         1   103
  FC.LOW.ENRICH                                          0     4
  FC.NO.ENRICH                                           0    31
D2V10, multiclass
                                           clus
vv                                          FC.HIGH.ENRICH FC.LOW.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE                       6             0
  ASIAN                                                 14             1
  BLACK OR AFRICAN AMERICAN                              8             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1             0
  WHITE                                                103             4
                                           clus
vv                                          FC.NO.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE                     2
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0
  WHITE                                               31
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                cls
clus              0  1
  FC.HIGH.ENRICH  9 93
  FC.LOW.ENRICH   0  6
  FC.NO.ENRICH    5 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    9   93
  FC.LOW.ENRICH     0    6
  FC.NO.ENRICH      5   36
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  9             0            5
  NOT HISPANIC OR LATINO             93             6           36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
D2V13, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 98 34
  FC.LOW.ENRICH   6  1
  FC.NO.ENRICH   35 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   98   34
  FC.LOW.ENRICH     6    1
  FC.NO.ENRICH     35   10
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  TUMOR FREE             98             6           35
  WITH TUMOR             34             1           10
[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
  FC.HIGH.ENRICH 11 63 60  1  5
  FC.LOW.ENRICH   1  5  1  0  0
  FC.NO.ENRICH    2 20 21  0  3
D2V14, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  G1             11             1            2
  G2             63             5           20
  G3             60             1           21
  G4              1             0            0
  GX              5             0            3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, continuous
D2V16, continuous
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            41              2             14 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CK     TCGA-C5-A7CL 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DR-A0ZM 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556     TCGA-EX-A1H5 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" 
    TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
D2V17, continuous
D2V18, continuous
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            37              2             13 
    TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A2LS 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ 
  "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CL 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DR-A0ZM     TCGA-DS-A5RQ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EA-A556     TCGA-EK-A2RA     TCGA-EX-A1H5     TCGA-FU-A2QG 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ     TCGA-FU-A3WB 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HM-A4S6 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB     TCGA-IR-A3LH 
  "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0     TCGA-MU-A5YI 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S     TCGA-RA-A741 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
D2V19, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 21  3
  FC.LOW.ENRICH   0  0
  FC.NO.ENRICH    5  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   21    3
  FC.LOW.ENRICH     0    0
  FC.NO.ENRICH      5    0
                         clus
vv                        FC.HIGH.ENRICH FC.NO.ENRICH
  COMPLETED AS PLANNED                21            5
  TREATMENT NOT COMPLETED              3            0
[1] 2 2
[1] FALSE
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FC.HIGH.ENRICH                                   0
  FC.LOW.ENRICH                                    0
  FC.NO.ENRICH                                     1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FC.HIGH.ENRICH                                   6                      22
  FC.LOW.ENRICH                                    0                       1
  FC.NO.ENRICH                                     1                       7
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FC.HIGH.ENRICH                       1                       7
  FC.LOW.ENRICH                        0                       0
  FC.NO.ENRICH                         0                       1
D2V26, multiclass
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            36              1             10 
    TCGA-EX-A449     TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1BK     TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2M1 
  "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A3HE     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7UC 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-DS-A3LQ     TCGA-EA-A50E     TCGA-EK-A2RC     TCGA-EK-A2RK 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EK-A2RN     TCGA-EX-A1H5     TCGA-FU-A3EO     TCGA-HM-A4S6 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-MU-A51Y 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
                                     clus
vv                                    FC.HIGH.ENRICH FC.NO.ENRICH
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              0            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              6            1
  OTHER LOCATION, SPECIFY                         22            7
  POSITIVE BLADDER MARGIN                          1            0
  POSITIVE VAGINAL MARGIN                          7            1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  FC.HIGH.ENRICH                                             1
  FC.LOW.ENRICH                                              0
  FC.NO.ENRICH                                               2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  FC.HIGH.ENRICH                                              9
  FC.LOW.ENRICH                                               1
  FC.NO.ENRICH                                                0
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  FC.HIGH.ENRICH                                                                                47
  FC.LOW.ENRICH                                                                                  4
  FC.NO.ENRICH                                                                                   9
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  FC.HIGH.ENRICH                                                                                           59
  FC.LOW.ENRICH                                                                                             0
  FC.NO.ENRICH                                                                                             29
D2V27, multiclass
                                                                                              clus
vv                                                                                             FC.HIGH.ENRICH
  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)                        47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             59
                                                                                              clus
vv                                                                                             FC.LOW.ENRICH
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             0
                                                                                              clus
vv                                                                                             FC.NO.ENRICH
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                          0
  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)           29
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V28, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 43 51
  FC.LOW.ENRICH   3  0
  FC.NO.ENRICH   17 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   43   51
  FC.LOW.ENRICH     3    0
  FC.NO.ENRICH     17   16
         clus
vv        FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ABSENT              43             3           17
  PRESENT             51             0           16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V29, continuous
D2V30, continuous
D2V31, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 32 59
  FC.LOW.ENRICH   2  3
  FC.NO.ENRICH    5 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   32   59
  FC.LOW.ENRICH     2    3
  FC.NO.ENRICH      5   24
                                          clus
vv                                         FC.HIGH.ENRICH FC.LOW.ENRICH
  KERATINIZING SQUAMOUS CELL CARCINOMA                 32             2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             59             3
                                          clus
vv                                         FC.NO.ENRICH
  KERATINIZING SQUAMOUS CELL CARCINOMA                5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA           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"
D2V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  FC.HIGH.ENRICH            6          32         28
  FC.LOW.ENRICH             0           0          1
  FC.NO.ENRICH              2          11         17
D2V33, multiclass
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            66              1             30 
    TCGA-EX-A69M     TCGA-C5-A1BI     TCGA-C5-A1BL     TCGA-C5-A1BN 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MN     TCGA-C5-A2LT 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HL     TCGA-C5-A7CG 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KM     TCGA-DR-A0ZL 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A7WF 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" 
    TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EA-A3QE     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-EA-A5O9     TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EK-A2R7 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EK-A3GK     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-EX-A69L     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
  "FC.NO.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-JW-A5VG     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-JW-A69B     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DV 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-UC-A7PD     TCGA-WL-A834 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
              clus
vv             FC.HIGH.ENRICH FC.NO.ENRICH
  CURRENT USER              6            2
  FORMER USER              32           11
  NEVER USED               28           17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V34, continuous
D2V35, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 63 11
  FC.LOW.ENRICH   2  0
  FC.NO.ENRICH   23  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   63   11
  FC.LOW.ENRICH     2    0
  FC.NO.ENRICH     23    5
         clus
vv        FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ABSENT              63             2           23
  PRESENT             11             0            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"
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  FC.HIGH.ENRICH           1        37     1
  FC.LOW.ENRICH            0         2     0
  FC.NO.ENRICH             3        14     0
D2V36, multiclass
[1] "Remove cluster labels:" "FC.LOW.ENRICH"         
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            39              2             17 
    TCGA-C5-A1BE     TCGA-C5-A1BI     TCGA-C5-A1BN     TCGA-C5-A1BQ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1M9     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MK 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1MN     TCGA-C5-A1MQ     TCGA-C5-A2LT     TCGA-C5-A2LX 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A2LY     TCGA-C5-A3HD     TCGA-C5-A7CK     TCGA-C5-A7CL 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UH     TCGA-C5-A7X3 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KM     TCGA-DR-A0ZM 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH"   "FC.NO.ENRICH" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-EA-A4BA     TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-HM-A3JJ 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-HM-A6W2     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-JW-A5VG 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
  "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
    TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852     TCGA-LP-A4AU 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-Q1-A73Q     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"FC.HIGH.ENRICH"   "FC.NO.ENRICH" "FC.HIGH.ENRICH"   "FC.NO.ENRICH" 
             clus
vv            FC.HIGH.ENRICH FC.NO.ENRICH
  CARBOPLATIN              1            3
  CISPLATIN               37           14
  OTHER                    1            0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
[1] "Remove cluster labels:" "FC.NO.ENRICH"          
clus
FC.HIGH.ENRICH   FC.NO.ENRICH 
             8              2 
    TCGA-C5-A1BN     TCGA-C5-A1MH     TCGA-C5-A1ML     TCGA-C5-A1MN 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
    TCGA-C5-A1MP     TCGA-EK-A2RO     TCGA-JW-A852     TCGA-MU-A51Y 
"FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" "FC.HIGH.ENRICH" 
D2V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  FC.HIGH.ENRICH       3        0         1         1       20        38
  FC.LOW.ENRICH        0        1         0         0        0         3
  FC.NO.ENRICH         1        0         0         0        8        12
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  FC.HIGH.ENRICH        19        3         3          5          3        11
  FC.LOW.ENRICH          0        1         1          0          0         0
  FC.NO.ENRICH          10        0         2          0          4         3
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  FC.HIGH.ENRICH         1         25         2         2
  FC.LOW.ENRICH          0          1         0         0
  FC.NO.ENRICH           0          3         0         3
D2V39, multiclass
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                 3             0            1
  STAGE IA                0             1            0
  STAGE IA1               1             0            0
  STAGE IA2               1             0            0
  STAGE IB               20             0            8
  STAGE IB1              38             3           12
  STAGE IB2              19             0           10
  STAGE II                3             1            0
  STAGE IIA               3             1            2
  STAGE IIA1              5             0            0
  STAGE IIA2              3             0            4
  STAGE IIB              11             0            3
  STAGE III               1             0            0
  STAGE IIIB             25             1            3
  STAGE IVA               2             0            0
  STAGE IVB               2             0            3
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
