[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/19775059/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/CESC-TP/20063368/APOBEC_clinical_corr_input_20063466/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   43  105 
   0 HIGH  LOW 
  46   43  105 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          141            40            13 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          141            40            13 
[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=148,	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=FALSE,	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=FALSE
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    34 10
  HIGH 35  6
  LOW  78 25
   0 HIGH  LOW 
  44   41  103 
   0 HIGH  LOW 
  10    6   25 
$`0`
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M2 
       67.46        57.73        73.18        73.45        78.35        33.24 
TCGA-C5-A7CG TCGA-C5-A7CM TCGA-DG-A2KJ TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF 
      210.67        20.35        95.11        28.90        22.98        16.18 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5O9 
        8.28        40.87        26.40        24.82        14.89        25.91 
TCGA-EA-A5ZD TCGA-EK-A2PK TCGA-EK-A2R9 TCGA-EK-A2RL TCGA-EX-A1H5 TCGA-EX-A449 
       27.29         0.39         0.13        47.77        20.35        14.70 
TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-HG-A2PA 
        8.32        16.11        36.26        26.14        35.44        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-JW-A5VG TCGA-JW-A5VH 
       21.67        20.78         9.44       147.39        27.42         3.29 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-Q1-A6DV TCGA-Q1-A73R 
       20.48        28.37        44.61        20.91        16.14        18.64 
TCGA-Q1-A73S TCGA-RA-A741 
       22.62        14.60 

$HIGH
TCGA-C5-A1BL TCGA-C5-A1BQ TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HE 
      173.29        19.86        38.99         2.43       100.14        18.02 
TCGA-C5-A7UH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-EA-A3HU 
      131.11        82.06        44.94        58.88        69.96        33.30 
TCGA-EA-A3Y4 TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R8 
       36.89        60.72         1.51         0.43         0.59         1.45 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK 
       40.96         4.31         0.10         0.43         0.10         0.49 
TCGA-EK-A3GM TCGA-FU-A3HY TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        0.76        31.36       137.16        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-MU-A51Y 
       36.36        21.44        15.58       209.59         0.30        28.08 
TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73O TCGA-Q1-A73P TCGA-UC-A7PF 
       54.81        16.41        14.07        15.88        93.99 

$LOW
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 
       36.56       144.16       177.04        82.85         5.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       46.32        30.21        35.01        53.16        35.61         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LX 
       20.91        40.93         3.58        33.90        44.22        83.05 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       38.43        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 
      134.33        15.48       147.35        17.19       155.77         9.34 
TCGA-DG-A2KH TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
        1.12        63.98        87.75        36.76        55.63        95.67 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
       16.83        17.52        39.55        37.35        30.90        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       13.05        25.02        24.56        31.73        26.01         0.30 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
        7.46        26.79        27.25        27.22        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2R7 TCGA-EK-A2RN 
       12.59        26.27         6.64        19.27         0.36         0.53 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
        0.03         7.92        15.22        19.79         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       19.04        20.98         1.48        16.14        28.31        14.01 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A4S6 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       10.55         1.12        14.93        66.81       129.37        96.95 
TCGA-JW-A5VI TCGA-JW-A852 TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       24.56         8.28        21.11        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.82        13.35        34.62        35.05        20.84        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD 
       15.95         9.04        17.56         9.34        19.59        11.67 
TCGA-WL-A834 
       26.01 

   0 HIGH  LOW 
0.13 0.10 0.03 
     0   HIGH    LOW 
210.67 209.59 177.04 
     0   HIGH    LOW 
25.115 29.850 23.670 
[1] "0.1 - 210.7 (25.1)" "0.1 - 209.6 (29.9)" "0.0 - 177.0 (23.7)"
D1V2, continuous
      vv
clus   T1 T2 T3+T4
  0    28 10     2
  HIGH 18 10     1
  LOW  58 20     2
D1V3, multiclass
       clus
vv       0 HIGH LOW
  T1    28   18  58
  T2    10   10  20
  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 20  7
  LOW  51 26
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      24   11
  HIGH   20    7
  LOW    51   26
   clus
vv   0 HIGH LOW
  0 24   20  51
  1 11    7  26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
      cls
clus    0  1
  0    19  3
  HIGH 15  1
  LOW  45  0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      19    3
  HIGH   15    1
  LOW    45    0
   clus
vv   0 HIGH LOW
  0 19   15  45
  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    13 12
  HIGH 10 13
  LOW  19 25
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      13   12
  HIGH   10   13
  LOW    19   25
     clus
vv     0 HIGH LOW
  NO  13   10  19
  YES 12   13  25
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  0                3                               30
  HIGH             0                               37
  LOW              1                               91
      vv
clus   ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  0                                                1
  HIGH                                             1
  LOW                                              3
      vv
clus   ENDOCERVICAL TYPE OF ADENOCARCINOMA
  0                                     10
  HIGH                                   4
  LOW                                    7
      vv
clus   ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  0                                            1
  HIGH                                         1
  LOW                                          0
      vv
clus   MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  0                                               1
  HIGH                                            0
  LOW                                             3
D1V7, multiclass
                                               clus
vv                                               0 HIGH LOW
  ADENOSQUAMOUS                                  3    0   1
  CERVICAL SQUAMOUS CELL CARCINOMA              30   37  91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE  1    1   3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA           10    4   7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX      1    1   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE   1    0   3
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  0                                   2     4                         6
  HIGH                                3     2                         3
  LOW                                 3    13                         7
      vv
clus   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  0                                            0    31
  HIGH                                         1    28
  LOW                                          0    79
D1V10, multiclass
                                           clus
vv                                           0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE           2    3   3
  ASIAN                                      4    2  13
  BLACK OR AFRICAN AMERICAN                  6    3   7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER  0    1   0
  WHITE                                     31   28  79
[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 22
  LOW   3 76
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   36
  HIGH    6   22
  LOW     3   76
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      5    6   3
  NOT HISPANIC OR LATINO 36   22  76
[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    33 10
  HIGH 24  9
  LOW  72 24
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      33   10
  HIGH   24    9
  LOW    72   24
            clus
vv            0 HIGH LOW
  TUMOR FREE 33   24  72
  WITH TUMOR 10    9  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
  0     2 20 21  0  3
  HIGH  4 14 22  1  1
  LOW   8 54 39  0  4
D1V14, multiclass
    clus
vv    0 HIGH LOW
  G1  2    4   8
  G2 20   14  54
  G3 21   22  39
  G4  0    1   0
  GX  3    1   4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
D1V16, continuous
      vv
clus   CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  0                                              8
  HIGH                                           6
  LOW                                           12
      vv
clus   CURRENT REFORMED SMOKER FOR > 15 YEARS
  0                                         2
  HIGH                                      1
  LOW                                       5
      vv
clus   CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  0                                                  0              9
  HIGH                                               0              5
  LOW                                                1             23
      vv
clus   LIFELONG NON-SMOKER
  0                     19
  HIGH                  20
  LOW                   54
D1V17, multiclass
                                                 clus
vv                                                 0 HIGH LOW
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS      8    6  12
  CURRENT REFORMED SMOKER FOR > 15 YEARS           2    1   5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED  0    0   1
  CURRENT SMOKER                                   9    5  23
  LIFELONG NON-SMOKER                             19   20  54
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V18, continuous
D1V19, binary
      cls
clus    0  1
  0     5  0
  HIGH  3  2
  LOW  18  1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5    0
  HIGH    3    2
  LOW    18    1
                         clus
vv                         0 HIGH LOW
  COMPLETED AS PLANNED     5    3  18
  TREATMENT NOT COMPLETED  0    2   1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                                    1                                   4
      vv
clus   OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  0                          7                       0                       1
  HIGH                       5                       0                       2
  LOW                       18                       1                       3
D1V26, multiclass
                                     clus
vv                                     0 HIGH LOW
  MACROSCOPIC PARAMETRIAL INVOLVEMENT  1    0   1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT  1    2   4
  OTHER LOCATION, SPECIFY              7    5  18
  POSITIVE BLADDER MARGIN              0    0   1
  POSITIVE VAGINAL MARGIN              1    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"
      vv
clus   INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  0                                                1
  HIGH                                             0
  LOW                                              1
      vv
clus   PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  0                                                 0
  HIGH                                              1
  LOW                                               9
      vv
clus   POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  0                                                                                    9
  HIGH                                                                                20
  LOW                                                                                 31
      vv
clus   PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  0                                                                                              29
  HIGH                                                                                           13
  LOW                                                                                            46
D1V27, multiclass
                                                                                              clus
vv                                                                                              0
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)             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)                                                  1
  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)   13
                                                                                              clus
vv                                                                                             LOW
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                  1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                 9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)             31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)  46
[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 11 15
  LOW  35 36
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      17   16
  HIGH   11   15
  LOW    35   36
         clus
vv         0 HIGH LOW
  ABSENT  17   11  35
  PRESENT 16   15  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"
D1V29, continuous
D1V30, continuous
D1V31, binary
      cls
clus    0  1
  0     5 24
  HIGH  9 18
  LOW  25 44
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       5   24
  HIGH    9   18
  LOW    25   44
                                          clus
vv                                          0 HIGH LOW
  KERATINIZING SQUAMOUS CELL CARCINOMA      5    9  25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA 24   18  44
[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            1           7          8
  LOW             5          25         21
D1V33, multiclass
              clus
vv              0 HIGH LOW
  CURRENT USER  2    1   5
  FORMER USER  11    7  25
  NEVER USED   17    8  21
[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 18  4
  LOW  47  7
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23    5
  HIGH   18    4
  LOW    47    7
         clus
vv         0 HIGH LOW
  ABSENT  23   18  47
  PRESENT  5    4   7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   CARBOPLATIN CISPLATIN OTHER
  0              3        14     0
  HIGH           1        12     0
  LOW            0        27     1
D1V36, multiclass
             clus
vv             0 HIGH LOW
  CARBOPLATIN  3    1   0
  CISPLATIN   14   12  27
  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"                      "HIGH"                  
clus
   0 HIGH  LOW 
   2    2    6 
TCGA-C5-A1BN TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-EK-A2RO TCGA-JW-A852 
       "LOW"        "LOW"        "LOW"        "LOW"        "LOW"        "LOW" 
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       0        0         0         1        4         8         7
  LOW        3        1         1         0       16        33        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        1         2          2          1         4         1          9
  LOW         3         2          3          2         7         0         17
      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    0   3
  STAGE IA    0    0   1
  STAGE IA1   0    0   1
  STAGE IA2   0    1   0
  STAGE IB    8    4  16
  STAGE IB1  12    8  33
  STAGE IB2  10    7  12
  STAGE II    0    1   3
  STAGE IIA   2    2   2
  STAGE IIA1  0    2   3
  STAGE IIA2  4    1   2
  STAGE IIB   3    4   7
  STAGE III   0    1   0
  STAGE IIIB  3    9  17
  STAGE IVA   0    0   2
  STAGE IVB   3    1   1
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
               sevent
clus2             0   1
  FC.HIGH.SIG   107  30
  FC.LOW.NONSIG  29  10
  FC.NEUTRAL     11   1
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          137            39            12 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           30            10             1 
$FC.HIGH.SIG
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       19.86        31.40        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        33.90        44.22        83.05       100.14        38.43 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CK 
       52.01        18.02        17.85        20.42       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH 
       15.48       147.35        17.19       131.11         9.34         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS 
       55.63        69.96        95.67        16.83        17.52        39.55 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.36        33.30        13.05        25.02        36.89 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE 
       24.56        31.73        26.01         0.30         7.46        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.22        24.00        13.48        60.72        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.43         0.59         0.36         1.45 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GJ 
       40.96         4.31         0.10         0.43         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.49         0.76         0.03         7.92        15.22        19.79 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TX 
        1.22        23.84        19.04        31.36        20.98         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A4S6 
       16.14        28.31        14.01        10.55         1.12        14.93 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 
       29.85        36.36        24.56        21.44        15.58         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       21.11       209.59        11.28        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.35        28.08        34.62        54.81        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95         9.04        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
        9.34        19.59        11.67        93.99        26.01 

$FC.LOW.NONSIG
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CM 
       67.46        57.73        78.35        33.24       210.67        20.35 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A410 
       28.90        22.98        16.18         8.28        40.87        26.40 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2PK TCGA-EK-A2R9 
       24.82        14.89        25.91        27.29         0.39         0.13 
TCGA-EK-A2RL TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3HZ 
       47.77        20.35        14.70         8.32        16.11        36.26 
TCGA-FU-A3TQ TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 
       26.14        35.44        25.41        21.67        20.78         9.44 
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 
       16.14        18.64        22.62 

$FC.NEUTRAL
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-DG-A2KJ TCGA-EA-A3HQ 
       73.18        73.45       101.82       155.77        95.11        37.35 
TCGA-EA-A5FO TCGA-EK-A2GZ TCGA-IR-A3L7 TCGA-LP-A4AW TCGA-MY-A5BE TCGA-RA-A741 
       26.79        12.59       147.39         0.89        35.05        14.60 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.03          0.13          0.89 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       209.59        210.67        155.77 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       23.670        22.980        55.265 
[1] "0.0 - 209.6 (23.7)" "0.1 - 210.7 (23.0)" "0.9 - 155.8 (55.3)"
D2V2, continuous
               vv
clus            T1 T2 T3+T4
  FC.HIGH.SIG   73 28     3
  FC.LOW.NONSIG 24 10     2
  FC.NEUTRAL     7  2     0
D2V3, multiclass
       clus
vv      FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1             73            24          7
  T2             28            10          2
  T3+T4           3             2          0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
               cls
clus             0  1
  FC.HIGH.SIG   67 32
  FC.LOW.NONSIG 22  9
  FC.NEUTRAL     6  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     67   32
  FC.LOW.NONSIG   22    9
  FC.NEUTRAL       6    3
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0          67            22          6
  1          32             9          3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
               cls
clus             0  1
  FC.HIGH.SIG   57  1
  FC.LOW.NONSIG 16  3
  FC.NEUTRAL     6  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     57    1
  FC.LOW.NONSIG   16    3
  FC.NEUTRAL       6    0
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0          57            16          6
  1           1             3          0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
               cls
clus             0  1
  FC.HIGH.SIG   27 35
  FC.LOW.NONSIG 13 10
  FC.NEUTRAL     2  5
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     27   35
  FC.LOW.NONSIG   13   10
  FC.NEUTRAL       2    5
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO           27            13          2
  YES          35            10          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            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  FC.HIGH.SIG               1                              121
  FC.LOW.NONSIG             3                               24
  FC.NEUTRAL                0                               13
               vv
clus            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  FC.HIGH.SIG                                               4
  FC.LOW.NONSIG                                             1
  FC.NEUTRAL                                                0
               vv
clus            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  FC.HIGH.SIG                                    11
  FC.LOW.NONSIG                                  10
  FC.NEUTRAL                                      0
               vv
clus            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  FC.HIGH.SIG                                           1
  FC.LOW.NONSIG                                         1
  FC.NEUTRAL                                            0
               vv
clus            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  FC.HIGH.SIG                                              3
  FC.LOW.NONSIG                                            1
  FC.NEUTRAL                                               0
D2V7, multiclass
                                               clus
vv                                              FC.HIGH.SIG FC.LOW.NONSIG
  ADENOSQUAMOUS                                           1             3
  CERVICAL SQUAMOUS CELL CARCINOMA                      121            24
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE           4             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                    11            10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX               1             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE            3             1
                                               clus
vv                                              FC.NEUTRAL
  ADENOSQUAMOUS                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                      13
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                    0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE           0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.SIG                                  6    14
  FC.LOW.NONSIG                                2     4
  FC.NEUTRAL                                   0     1
               vv
clus            BLACK OR AFRICAN AMERICAN
  FC.HIGH.SIG                           8
  FC.LOW.NONSIG                         5
  FC.NEUTRAL                            3
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FC.HIGH.SIG                                           1   103
  FC.LOW.NONSIG                                         0    27
  FC.NEUTRAL                                            0     8
D2V10, multiclass
                                           clus
vv                                          FC.HIGH.SIG FC.LOW.NONSIG
  AMERICAN INDIAN OR ALASKA NATIVE                    6             2
  ASIAN                                              14             4
  BLACK OR AFRICAN AMERICAN                           8             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             0
  WHITE                                             103            27
                                           clus
vv                                          FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE                   0
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0
  WHITE                                              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"
D2V11, binary
               cls
clus             0  1
  FC.HIGH.SIG    9 92
  FC.LOW.NONSIG  5 32
  FC.NEUTRAL     0 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      9   92
  FC.LOW.NONSIG    5   32
  FC.NEUTRAL       0   10
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               9             5          0
  NOT HISPANIC OR LATINO          92            32         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"
D2V12, continuous
D2V13, binary
               cls
clus             0  1
  FC.HIGH.SIG   90 32
  FC.LOW.NONSIG 28  9
  FC.NEUTRAL    11  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     90   32
  FC.LOW.NONSIG   28    9
  FC.NEUTRAL      11    2
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  TUMOR FREE          90            28         11
  WITH TUMOR          32             9          2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            G1 G2 G3 G4 GX
  FC.HIGH.SIG   11 63 60  1  5
  FC.LOW.NONSIG  2 20 16  0  2
  FC.NEUTRAL     1  5  6  0  1
D2V14, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  G1          11             2          1
  G2          63            20          5
  G3          60            16          6
  G4           1             0          0
  GX           5             2          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"
D2V15, continuous
[1] "Remove cluster labels:" "FC.NEUTRAL"            
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           20             7             2 
   TCGA-BI-A0VR    TCGA-C5-A1BJ    TCGA-C5-A1BL    TCGA-C5-A1BQ    TCGA-C5-A1ME 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A1MF    TCGA-C5-A1MH    TCGA-C5-A2M2    TCGA-C5-A3HD    TCGA-C5-A7CM 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-C5-A7CO    TCGA-DG-A2KK    TCGA-DS-A3LQ    TCGA-EK-A2RA    TCGA-EX-A69M 
  "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG" 
   TCGA-FU-A2QG    TCGA-FU-A3TX    TCGA-FU-A3WB    TCGA-HM-A3JK    TCGA-HM-A4S6 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" "FC.LOW.NONSIG"   "FC.HIGH.SIG" 
   TCGA-IR-A3LB    TCGA-IR-A3LH    TCGA-JX-A3Q0    TCGA-MU-A5YI    TCGA-Q1-A6DW 
  "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG"   "FC.HIGH.SIG" 
   TCGA-Q1-A73S    TCGA-WL-A834 
"FC.LOW.NONSIG"   "FC.HIGH.SIG" 
D2V16, continuous
               vv
clus            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  FC.HIGH.SIG                                            18
  FC.LOW.NONSIG                                           6
  FC.NEUTRAL                                              2
               vv
clus            CURRENT REFORMED SMOKER FOR > 15 YEARS
  FC.HIGH.SIG                                        6
  FC.LOW.NONSIG                                      2
  FC.NEUTRAL                                         0
               vv
clus            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  FC.HIGH.SIG                                                 1             26
  FC.LOW.NONSIG                                               0              7
  FC.NEUTRAL                                                  0              4
               vv
clus            LIFELONG NON-SMOKER
  FC.HIGH.SIG                    70
  FC.LOW.NONSIG                  19
  FC.NEUTRAL                      4
D2V17, multiclass
                                                 clus
vv                                                FC.HIGH.SIG FC.LOW.NONSIG
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS              18             6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                    6             2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED           1             0
  CURRENT SMOKER                                           26             7
  LIFELONG NON-SMOKER                                      70            19
                                                 clus
vv                                                FC.NEUTRAL
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS              2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                   0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED          0
  CURRENT SMOKER                                           4
  LIFELONG NON-SMOKER                                      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"
D2V18, continuous
D2V19, binary
               cls
clus             0  1
  FC.HIGH.SIG   21  3
  FC.LOW.NONSIG  4  0
  FC.NEUTRAL     1  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     21    3
  FC.LOW.NONSIG    4    0
  FC.NEUTRAL       1    0
                         clus
vv                        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  COMPLETED AS PLANNED             21             4          1
  TREATMENT NOT COMPLETED           3             0          0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
               vv
clus            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FC.HIGH.SIG                                     1
  FC.LOW.NONSIG                                   1
  FC.NEUTRAL                                      0
               vv
clus            MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FC.HIGH.SIG                                     6                      22
  FC.LOW.NONSIG                                   1                       5
  FC.NEUTRAL                                      0                       3
               vv
clus            POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FC.HIGH.SIG                         1                       5
  FC.LOW.NONSIG                       0                       1
  FC.NEUTRAL                          0                       0
D2V26, multiclass
                                     clus
vv                                    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  MACROSCOPIC PARAMETRIAL INVOLVEMENT           1             1          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT           6             1          0
  OTHER LOCATION, SPECIFY                      22             5          3
  POSITIVE BLADDER MARGIN                       1             0          0
  POSITIVE VAGINAL MARGIN                       5             1          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)
  FC.HIGH.SIG                                               1
  FC.LOW.NONSIG                                             1
  FC.NEUTRAL                                                0
               vv
clus            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  FC.HIGH.SIG                                                9
  FC.LOW.NONSIG                                              0
  FC.NEUTRAL                                                 1
               vv
clus            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  FC.HIGH.SIG                                                                                  47
  FC.LOW.NONSIG                                                                                 9
  FC.NEUTRAL                                                                                    4
               vv
clus            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  FC.HIGH.SIG                                                                                             59
  FC.LOW.NONSIG                                                                                           25
  FC.NEUTRAL                                                                                               4
D2V27, multiclass
                                                                                              clus
vv                                                                                             FC.HIGH.SIG
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                         9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                     47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)          59
                                                                                              clus
vv                                                                                             FC.LOW.NONSIG
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            25
                                                                                              clus
vv                                                                                             FC.NEUTRAL
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                        1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                     4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)          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"
D2V28, binary
               cls
clus             0  1
  FC.HIGH.SIG   43 51
  FC.LOW.NONSIG 15 14
  FC.NEUTRAL     5  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     43   51
  FC.LOW.NONSIG   15   14
  FC.NEUTRAL       5    2
         clus
vv        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ABSENT           43            15          5
  PRESENT          51            14          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"
D2V29, continuous
D2V30, continuous
D2V31, binary
               cls
clus             0  1
  FC.HIGH.SIG   32 59
  FC.LOW.NONSIG  4 21
  FC.NEUTRAL     3  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     32   59
  FC.LOW.NONSIG    4   21
  FC.NEUTRAL       3    6
                                          clus
vv                                         FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  KERATINIZING SQUAMOUS CELL CARCINOMA              32             4          3
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA          59            21          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"
D2V32, continuous
               vv
clus            CURRENT USER FORMER USER NEVER USED
  FC.HIGH.SIG              6          32         28
  FC.LOW.NONSIG            1          10         16
  FC.NEUTRAL               1           1          2
D2V33, multiclass
              clus
vv             FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  CURRENT USER           6             1          1
  FORMER USER           32            10          1
  NEVER USED            28            16          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"
D2V34, continuous
D2V35, binary
               cls
clus             0  1
  FC.HIGH.SIG   63 11
  FC.LOW.NONSIG 19  5
  FC.NEUTRAL     6  0
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     63   11
  FC.LOW.NONSIG   19    5
  FC.NEUTRAL       6    0
         clus
vv        FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ABSENT           63            19          6
  PRESENT          11             5          0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CARBOPLATIN CISPLATIN OTHER
  FC.HIGH.SIG             1        37     1
  FC.LOW.NONSIG           3        11     0
  FC.NEUTRAL              0         5     0
D2V36, multiclass
             clus
vv            FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  CARBOPLATIN           1             3          0
  CISPLATIN            37            11          5
  OTHER                 1             0          0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
[1] "Remove cluster labels:" "FC.LOW.NONSIG"         
clus
  FC.HIGH.SIG FC.LOW.NONSIG 
            8             2 
 TCGA-C5-A1BN  TCGA-C5-A1MH  TCGA-C5-A1ML  TCGA-C5-A1MN  TCGA-C5-A1MP 
"FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" 
 TCGA-EK-A2RO  TCGA-JW-A852  TCGA-MU-A51Y 
"FC.HIGH.SIG" "FC.HIGH.SIG" "FC.HIGH.SIG" 
D2V38, continuous
               vv
clus            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  FC.HIGH.SIG         3        0         1         1       20        38
  FC.LOW.NONSIG       1        0         0         0        5        11
  FC.NEUTRAL          0        1         0         0        3         4
               vv
clus            STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  FC.HIGH.SIG          19        3         3          5          3        11
  FC.LOW.NONSIG        10        0         2          0          4         2
  FC.NEUTRAL            0        1         1          0          0         1
               vv
clus            STAGE III STAGE IIIB STAGE IVA STAGE IVB
  FC.HIGH.SIG           1         25         2         2
  FC.LOW.NONSIG         0          2         0         3
  FC.NEUTRAL            0          2         0         0
D2V39, multiclass
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I              3             1          0
  STAGE IA             0             0          1
  STAGE IA1            1             0          0
  STAGE IA2            1             0          0
  STAGE IB            20             5          3
  STAGE IB1           38            11          4
  STAGE IB2           19            10          0
  STAGE II             3             0          1
  STAGE IIA            3             2          1
  STAGE IIA1           5             0          0
  STAGE IIA2           3             4          0
  STAGE IIB           11             2          1
  STAGE III            1             0          0
  STAGE IIIB          25             2          2
  STAGE IVA            2             0          0
  STAGE IVB            2             3          0
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
