[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[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/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/22574677/transformed.cor.cli.txt"

nPatients in clinical file=307, in cluster file=194, common to both=194
[1]  20 194
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             183 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             178 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            22            172 
  MLL2 MUTATED MLL2 WILD-TYPE 
            22            172 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            165 
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            165 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
[1] "FAT2 MUTATION ANALYSIS"
[1] 3
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            183 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              185 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              185 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
[1] "C3ORF70 MUTATION ANALYSIS"
[1] 3
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                4               190 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                4               190 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
[1] "IFNGR1 MUTATION ANALYSIS"
[1] 3
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
[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 = PTEN MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    11   4
  PTEN WILD-TYPE 139  38
  PTEN MUTATED PTEN WILD-TYPE 
            15            177 
  PTEN MUTATED PTEN WILD-TYPE 
             4             38 
$`PTEN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A3HL TCGA-C5-A7CL TCGA-EA-A4BA 
       49.48        82.85        19.86        20.42        15.48        24.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2PM TCGA-EK-A2RK TCGA-FU-A23K TCGA-FU-A3HZ 
       14.89        26.79         0.59         0.43        12.23        36.26 
TCGA-FU-A3TQ TCGA-JW-A5VH TCGA-Q1-A6DW 
       26.14         3.29        17.56 

$`PTEN WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VS TCGA-BI-A20A 
       12.59        14.70         8.32         1.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       11.44        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29         5.46        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       35.01        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS 
        2.43        20.91        40.93         3.58        33.90        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH 
       33.24        52.01        18.02        17.85       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
      131.11         9.34         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63       117.99 
TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      118.65        28.90        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
        8.28        39.55        40.87        37.35        30.90        31.36 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       33.30        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD 
       31.73        26.01        12.13         7.46        25.91        27.29 
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-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
        6.64         1.51        19.27         0.39         0.43         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        1.87         1.74        47.77         1.64         2.33         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.49         0.89        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI 
       19.79        23.84        19.04        16.11        31.36        20.98 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         9.44       147.39 
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-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       29.85        36.36        27.42        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        28.37         8.28        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.35        28.08        34.62        54.81        35.05        20.84 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O 
       15.58        16.41        15.95         9.04        16.14        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  PTEN MUTATED PTEN WILD-TYPE 
          0.43           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         82.85         210.67 
  PTEN MUTATED PTEN WILD-TYPE 
         19.86          24.00 
[1] "0.4 - 82.8 (19.9)"  "0.1 - 210.7 (24.0)"
[1] "hr=" "1.9"
D1V2, continuous
                vv
clus             T1 T2 T3+T4
  PTEN MUTATED    6  4     1
  PTEN WILD-TYPE 98 36     4
D1V3, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T1               6             98
  T2               4             36
  T3+T4            1              4
[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"
D1V4, binary
                cls
clus              0  1
  PTEN MUTATED    6  4
  PTEN WILD-TYPE 89 40
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6    4
  PTEN WILD-TYPE   89   40
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            6             89
  1            4             40
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus              0  1
  PTEN MUTATED    5  1
  PTEN WILD-TYPE 74  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    1
  PTEN WILD-TYPE   74    3
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5             74
  1            1              3
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  PTEN MUTATED    1  5
  PTEN WILD-TYPE 39 47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    5
  PTEN WILD-TYPE   39   47
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             1             39
  YES            5             47
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  PTEN MUTATED               0                               13
  PTEN WILD-TYPE             4                              145
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  PTEN MUTATED                                               0
  PTEN WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  PTEN MUTATED                                     1
  PTEN WILD-TYPE                                  20
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  PTEN MUTATED                                           1
  PTEN WILD-TYPE                                         1
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  PTEN MUTATED                                              0
  PTEN WILD-TYPE                                            4
D1V7, multiclass
                                               clus
vv                                              PTEN MUTATED PTEN WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                        13            145
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      1             20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              4
[1] 6 2
[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
  PTEN MUTATED                                  1     0
  PTEN WILD-TYPE                                7    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  PTEN MUTATED                           1
  PTEN WILD-TYPE                        15
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTEN MUTATED                                           0    13
  PTEN WILD-TYPE                                         1   125
D1V10, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              7
  ASIAN                                                0             19
  BLACK OR AFRICAN AMERICAN                            1             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            125
[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"
D1V11, binary
                cls
clus               0   1
  PTEN MUTATED     1  10
  PTEN WILD-TYPE  13 125
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   10
  PTEN WILD-TYPE   13  125
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO           10            125
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                cls
clus               0   1
  PTEN MUTATED    10   3
  PTEN WILD-TYPE 129  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     10    3
  PTEN WILD-TYPE  129   42
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  TUMOR FREE           10            129
  WITH TUMOR            3             42
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  PTEN MUTATED    0  8  6  0  1
  PTEN WILD-TYPE 14 80 76  1  7
D1V14, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  G1            0             14
  G2            8             80
  G3            6             76
  G4            0              1
  GX            1              7
[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"
D1V15, continuous
D1V16, continuous
D1V17, continuous
D1V18, continuous
D1V19, binary
                cls
clus              0  1
  PTEN MUTATED    2  0
  PTEN WILD-TYPE 24  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2    0
  PTEN WILD-TYPE   24    3
                         clus
vv                        PTEN MUTATED PTEN WILD-TYPE
  COMPLETED AS PLANNED               2             24
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  PTEN MUTATED                                     0
  PTEN WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  PTEN MUTATED                                     0                       1
  PTEN WILD-TYPE                                   7                      29
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  PTEN MUTATED                         0                       2
  PTEN WILD-TYPE                       1                       6
D1V26, multiclass
                                     clus
vv                                    PTEN MUTATED PTEN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            0              7
  OTHER LOCATION, SPECIFY                        1             29
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        2              6
[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)
  PTEN MUTATED                                               0
  PTEN WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  PTEN MUTATED                                                0
  PTEN WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  PTEN MUTATED                                                                                   9
  PTEN WILD-TYPE                                                                                51
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  PTEN MUTATED                                                                                              5
  PTEN WILD-TYPE                                                                                           83
D1V27, multiclass
                                                                                              clus
vv                                                                                             PTEN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                          0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                       9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            5
                                                                                              clus
vv                                                                                             PTEN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V28, binary
                cls
clus              0  1
  PTEN MUTATED    5  5
  PTEN WILD-TYPE 58 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    5
  PTEN WILD-TYPE   58   62
         clus
vv        PTEN MUTATED PTEN WILD-TYPE
  ABSENT             5             58
  PRESENT            5             62
[1] 2 2
[1] FALSE
D1V29, continuous
D1V30, continuous
D1V31, binary
                cls
clus              0  1
  PTEN MUTATED    4  9
  PTEN WILD-TYPE 35 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    9
  PTEN WILD-TYPE   35   77
                                          clus
vv                                         PTEN MUTATED PTEN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                4             35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            9             77
[1] 2 2
[1] FALSE
D1V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  PTEN MUTATED              0           0          3
  PTEN WILD-TYPE            8          43         43
D1V33, multiclass
              clus
vv             PTEN MUTATED PTEN WILD-TYPE
  CURRENT USER            0              8
  FORMER USER             0             43
  NEVER USED              3             43
[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"
D1V34, continuous
D1V35, binary
                cls
clus              0  1
  PTEN MUTATED    5  4
  PTEN WILD-TYPE 83 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    4
  PTEN WILD-TYPE   83   12
         clus
vv        PTEN MUTATED PTEN WILD-TYPE
  ABSENT             5             83
  PRESENT            4             12
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  PTEN MUTATED             2         3     0
  PTEN WILD-TYPE           2        50     1
D1V36, multiclass
             clus
vv            PTEN MUTATED PTEN WILD-TYPE
  CARBOPLATIN            2              2
  CISPLATIN              3             50
  OTHER                  0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
D1V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  PTEN MUTATED         1        0         0         1        1         2
  PTEN WILD-TYPE       3        1         1         0       27        51
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  PTEN MUTATED           2        0         0          0          1         1
  PTEN WILD-TYPE        27        4         6          5          6        13
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  PTEN MUTATED           0          5         0         1
  PTEN WILD-TYPE         1         24         2         4
D1V39, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               1              3
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             1              0
  STAGE IB              1             27
  STAGE IB1             2             51
  STAGE IB2             2             27
  STAGE II              0              4
  STAGE IIA             0              6
  STAGE IIA1            0              5
  STAGE IIA2            1              6
  STAGE IIB             1             13
  STAGE III             0              1
  STAGE IIIB            5             24
  STAGE IVA             0              2
  STAGE IVB             1              4
[1] 16  2
[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 = HLA-B MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     9   2
  HLA-B WILD-TYPE 141  40
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             181 
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              40 
$`HLA-B MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1ML TCGA-FU-A3TQ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
      144.16        20.91        26.14        78.71        29.85        36.36 
TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-Q1-A5R3 TCGA-Q1-A73O 
       24.56        15.58       209.59        15.95        14.07 

$`HLA-B WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74        36.56       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ 
       35.61         0.46         2.43        40.93         3.58        33.90 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH 
      147.35        17.19       155.77       131.11         9.34         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76        55.63       117.99       118.65        28.90        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.36        33.30        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
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-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
        6.64         1.51        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.89         1.45         0.13        40.96         0.30         4.24 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         1.87         1.74         0.43        47.77         1.64 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
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-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ 
       16.11        31.36        36.26        20.98        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
       14.01        35.44        10.55         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ 
      129.37        96.95        81.96        27.42         3.29        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV 
       20.48        28.37         8.28        21.11        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       28.08        34.62        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
       16.41         9.04        16.14        17.56        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-WL-A834 
       26.01 

  HLA-B MUTATED HLA-B WILD-TYPE 
          14.07            0.07 
  HLA-B MUTATED HLA-B WILD-TYPE 
         209.59          210.67 
  HLA-B MUTATED HLA-B WILD-TYPE 
          26.14           22.98 
[1] "14.1 - 209.6 (26.1)" "0.1 - 210.7 (23.0)" 
[1] "hr=" "1.6"
D2V2, continuous
                 vv
clus               T1  T2 T3+T4
  HLA-B MUTATED     3   3     1
  HLA-B WILD-TYPE 101  37     4
D2V3, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T1                3             101
  T2                3              37
  T3+T4             1               4
[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"
D2V4, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  1
  HLA-B WILD-TYPE 91 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    1
  HLA-B WILD-TYPE   91   43
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             4              91
  1             1              43
[1] 2 2
[1] FALSE
D2V5, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  0
  HLA-B WILD-TYPE 75  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    0
  HLA-B WILD-TYPE   75    4
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             4              75
  1             0               4
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  5
  HLA-B WILD-TYPE 38 47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    5
  HLA-B WILD-TYPE   38   47
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              2              38
  YES             5              47
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  HLA-B MUTATED               0                               11
  HLA-B WILD-TYPE             4                              147
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  HLA-B MUTATED                                               0
  HLA-B WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  HLA-B MUTATED                                     0
  HLA-B WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  HLA-B MUTATED                                           0
  HLA-B WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  HLA-B MUTATED                                              0
  HLA-B WILD-TYPE                                            4
D2V7, multiclass
                                               clus
vv                                              HLA-B MUTATED HLA-B WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                         11             147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[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
  HLA-B MUTATED                                  2     0
  HLA-B WILD-TYPE                                6    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  HLA-B MUTATED                           2
  HLA-B WILD-TYPE                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-B MUTATED                                           0     6
  HLA-B WILD-TYPE                                         1   132
D2V10, multiclass
                                           clus
vv                                          HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      2               6
  ASIAN                                                 0              19
  BLACK OR AFRICAN AMERICAN                             2              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             132
[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"
D2V11, binary
                 cls
clus                0   1
  HLA-B MUTATED     3   3
  HLA-B WILD-TYPE  11 132
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    3
  HLA-B WILD-TYPE   11  132
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 3              11
  NOT HISPANIC OR LATINO             3             132
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   3
  HLA-B WILD-TYPE 131  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    3
  HLA-B WILD-TYPE  131   42
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  TUMOR FREE             8             131
  WITH TUMOR             3              42
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  HLA-B MUTATED    1  5  3  1  1
  HLA-B WILD-TYPE 13 83 79  0  7
D2V14, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  G1             1              13
  G2             5              83
  G3             3              79
  G4             1               0
  GX             1               7
[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"
D2V15, continuous
D2V16, continuous
D2V17, continuous
D2V18, continuous
D2V19, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  0
  HLA-B WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    0
  HLA-B WILD-TYPE   24    3
                         clus
vv                        HLA-B MUTATED HLA-B WILD-TYPE
  COMPLETED AS PLANNED                2              24
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  HLA-B MUTATED                                     0
  HLA-B WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  HLA-B MUTATED                                     1                       0
  HLA-B WILD-TYPE                                   6                      30
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  HLA-B MUTATED                         0                       1
  HLA-B WILD-TYPE                       1                       7
D2V26, multiclass
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              45 
     TCGA-EX-A449      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DR-A0ZM 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E      TCGA-EK-A2RC 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-EK-A2RK      TCGA-EK-A2RN      TCGA-EX-A1H5      TCGA-FU-A3EO 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LI      TCGA-MU-A51Y      TCGA-UC-A7PD 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-WL-A834 
"HLA-B WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  HLA-B MUTATED                                               0
  HLA-B WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  HLA-B MUTATED                                                0
  HLA-B WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  HLA-B MUTATED                                                                                   6
  HLA-B WILD-TYPE                                                                                54
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  HLA-B MUTATED                                                                                              5
  HLA-B WILD-TYPE                                                                                           83
D2V27, multiclass
                                                                                              clus
vv                                                                                             HLA-B MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             5
                                                                                              clus
vv                                                                                             HLA-B WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V28, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  2
  HLA-B WILD-TYPE 61 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    2
  HLA-B WILD-TYPE   61   65
         clus
vv        HLA-B MUTATED HLA-B WILD-TYPE
  ABSENT              2              61
  PRESENT             2              65
[1] 2 2
[1] FALSE
D2V29, continuous
D2V30, continuous
D2V31, binary
                 cls
clus               0  1
  HLA-B MUTATED    1  5
  HLA-B WILD-TYPE 38 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      1    5
  HLA-B WILD-TYPE   38   81
                                          clus
vv                                         HLA-B MUTATED HLA-B WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 1              38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             5              81
[1] 2 2
[1] FALSE
D2V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  HLA-B MUTATED              0           3          2
  HLA-B WILD-TYPE            8          40         44
D2V33, multiclass
              clus
vv             HLA-B MUTATED HLA-B WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              3              40
  NEVER USED               2              44
[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
  HLA-B MUTATED    4  1
  HLA-B WILD-TYPE 84 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    1
  HLA-B WILD-TYPE   84   15
         clus
vv        HLA-B MUTATED HLA-B WILD-TYPE
  ABSENT              4              84
  PRESENT             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  HLA-B MUTATED             0         4     0
  HLA-B WILD-TYPE           4        49     1
D2V36, multiclass
             clus
vv            HLA-B MUTATED HLA-B WILD-TYPE
  CARBOPLATIN             0               4
  CISPLATIN               4              49
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              1               9 
     TCGA-C5-A1BN      TCGA-C5-A1MH      TCGA-C5-A1MN      TCGA-C5-A1MP 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-HM-A3JK      TCGA-JW-A852      TCGA-JX-A3Q8 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-MU-A51Y 
"HLA-B WILD-TYPE" 
D2V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  HLA-B MUTATED         0        0         0         0        0         1
  HLA-B WILD-TYPE       4        1         1         1       28        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  HLA-B MUTATED           4        0         0          1          0         2
  HLA-B WILD-TYPE        25        4         6          4          7        12
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  HLA-B MUTATED           1          1         0         0
  HLA-B WILD-TYPE         0         28         2         5
D2V39, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               0              28
  STAGE IB1              1              52
  STAGE IB2              4              25
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             1               4
  STAGE IIA2             0               7
  STAGE IIB              2              12
  STAGE III              1               0
  STAGE IIIB             1              28
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = HLA-A MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    13   2
  HLA-A WILD-TYPE 137  40
  HLA-A MUTATED HLA-A WILD-TYPE 
             15             177 
  HLA-A MUTATED HLA-A WILD-TYPE 
              2              40 
$`HLA-A MUTATED`
TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A1MQ TCGA-C5-A3HD TCGA-C5-A3HL TCGA-C5-A7CO 
       18.74        19.86        33.90        52.01        20.42       147.35 
TCGA-DR-A0ZM TCGA-EA-A3QE TCGA-EK-A2PL TCGA-EX-A69L TCGA-FU-A3HZ TCGA-IR-A3LH 
       58.88        25.02         0.43        19.79        36.26        78.71 
TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-Q1-A73O 
       15.58       209.59        14.07 

$`HLA-A WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
      173.29        82.85         5.46        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       33.24        18.02        17.85       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35        17.19       155.77       131.11 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        9.34         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       87.75        36.76        55.63       117.99       118.65        28.90 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
       40.87        37.35        30.90        31.36        33.30        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
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-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.39         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        1.87         1.74         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.22        12.23        23.84        19.04        16.11        31.36 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       20.98        26.14        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       10.55         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 
       21.44        20.48        28.37         8.28        21.11        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.35        28.08        34.62        54.81        35.05        20.84 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  HLA-A MUTATED HLA-A WILD-TYPE 
           0.43            0.07 
  HLA-A MUTATED HLA-A WILD-TYPE 
         209.59          210.67 
  HLA-A MUTATED HLA-A WILD-TYPE 
          25.02           23.67 
[1] "0.4 - 209.6 (25.0)" "0.1 - 210.7 (23.7)"
[1] "hr=" "2.1"
D3V2, continuous
                 vv
clus              T1 T2 T3+T4
  HLA-A MUTATED    5  4     1
  HLA-A WILD-TYPE 99 36     4
D3V3, multiclass
       clus
vv      HLA-A MUTATED HLA-A WILD-TYPE
  T1                5              99
  T2                4              36
  T3+T4             1               4
[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"
D3V4, binary
                 cls
clus               0  1
  HLA-A MUTATED   10  0
  HLA-A WILD-TYPE 85 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     10    0
  HLA-A WILD-TYPE   85   44
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            10              85
  1             0              44
[1] 2 2
[1] FALSE
D3V5, binary
                 cls
clus               0  1
  HLA-A MUTATED    8  0
  HLA-A WILD-TYPE 71  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      8    0
  HLA-A WILD-TYPE   71    4
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             8              71
  1             0               4
[1] 2 2
[1] FALSE
D3V6, binary
                 cls
clus               0  1
  HLA-A MUTATED    3  5
  HLA-A WILD-TYPE 37 47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3    5
  HLA-A WILD-TYPE   37   47
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              3              37
  YES             5              47
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  HLA-A MUTATED               0                               16
  HLA-A WILD-TYPE             4                              142
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  HLA-A MUTATED                                               0
  HLA-A WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  HLA-A MUTATED                                     0
  HLA-A WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  HLA-A MUTATED                                           0
  HLA-A WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  HLA-A MUTATED                                              0
  HLA-A WILD-TYPE                                            4
D3V7, multiclass
                                               clus
vv                                              HLA-A MUTATED HLA-A WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                         16             142
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  1     2
  HLA-A WILD-TYPE                                7    17
                 vv
clus              BLACK OR AFRICAN AMERICAN
  HLA-A MUTATED                           2
  HLA-A WILD-TYPE                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-A MUTATED                                           0    10
  HLA-A WILD-TYPE                                         1   128
D3V10, multiclass
                                           clus
vv                                          HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               7
  ASIAN                                                 2              17
  BLACK OR AFRICAN AMERICAN                             2              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             128
[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"
D3V11, binary
                 cls
clus                0   1
  HLA-A MUTATED     2  11
  HLA-A WILD-TYPE  12 124
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      2   11
  HLA-A WILD-TYPE   12  124
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            11             124
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                 cls
clus                0   1
  HLA-A MUTATED    14   2
  HLA-A WILD-TYPE 125  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     14    2
  HLA-A WILD-TYPE  125   43
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  TUMOR FREE            14             125
  WITH TUMOR             2              43
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  HLA-A MUTATED    2  9  2  1  1
  HLA-A WILD-TYPE 12 79 80  0  7
D3V14, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  G1             2              12
  G2             9              79
  G3             2              80
  G4             1               0
  GX             1               7
[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"
D3V15, continuous
D3V16, continuous
D3V17, continuous
D3V18, continuous
D3V19, binary
                 cls
clus               0  1
  HLA-A MUTATED    5  0
  HLA-A WILD-TYPE 21  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      5    0
  HLA-A WILD-TYPE   21    3
                         clus
vv                        HLA-A MUTATED HLA-A WILD-TYPE
  COMPLETED AS PLANNED                5              21
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D3V20, continuous
D3V21, continuous
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  HLA-A MUTATED                                     0
  HLA-A WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  HLA-A MUTATED                                     1                       2
  HLA-A WILD-TYPE                                   6                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  HLA-A MUTATED                         0                       1
  HLA-A WILD-TYPE                       1                       7
D3V26, multiclass
                                     clus
vv                                    HLA-A MUTATED HLA-A WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             1               6
  OTHER LOCATION, SPECIFY                         2              28
  POSITIVE BLADDER MARGIN                         0               1
  POSITIVE VAGINAL MARGIN                         1               7
[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)
  HLA-A MUTATED                                               0
  HLA-A WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  HLA-A MUTATED                                                0
  HLA-A WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  HLA-A MUTATED                                                                                   6
  HLA-A WILD-TYPE                                                                                54
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  HLA-A MUTATED                                                                                              5
  HLA-A WILD-TYPE                                                                                           83
D3V27, multiclass
                                                                                              clus
vv                                                                                             HLA-A MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             5
                                                                                              clus
vv                                                                                             HLA-A WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V28, binary
                 cls
clus               0  1
  HLA-A MUTATED    4  3
  HLA-A WILD-TYPE 59 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4    3
  HLA-A WILD-TYPE   59   64
         clus
vv        HLA-A MUTATED HLA-A WILD-TYPE
  ABSENT              4              59
  PRESENT             3              64
[1] 2 2
[1] FALSE
D3V29, continuous
D3V30, continuous
D3V31, binary
                 cls
clus               0  1
  HLA-A MUTATED    4  7
  HLA-A WILD-TYPE 35 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4    7
  HLA-A WILD-TYPE   35   79
                                          clus
vv                                         HLA-A MUTATED HLA-A WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 4              35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             7              79
[1] 2 2
[1] FALSE
D3V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  HLA-A MUTATED              0           3          4
  HLA-A WILD-TYPE            8          40         42
D3V33, multiclass
              clus
vv             HLA-A MUTATED HLA-A WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              3              40
  NEVER USED               4              42
[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"
D3V34, continuous
D3V35, binary
                 cls
clus               0  1
  HLA-A MUTATED    5  2
  HLA-A WILD-TYPE 83 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      5    2
  HLA-A WILD-TYPE   83   14
         clus
vv        HLA-A MUTATED HLA-A WILD-TYPE
  ABSENT              5              83
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  HLA-A MUTATED             0         7     0
  HLA-A WILD-TYPE           4        46     1
D3V36, multiclass
             clus
vv            HLA-A MUTATED HLA-A WILD-TYPE
  CARBOPLATIN             0               4
  CISPLATIN               7              46
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V37, continuous
D3V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  HLA-A MUTATED         0        0         0         0        3         1
  HLA-A WILD-TYPE       4        1         1         1       25        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  HLA-A MUTATED           4        0         1          1          1         1
  HLA-A WILD-TYPE        25        4         5          4          6        13
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  HLA-A MUTATED           1          3         0         0
  HLA-A WILD-TYPE         0         26         2         5
D3V39, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               3              25
  STAGE IB1              1              52
  STAGE IB2              4              25
  STAGE II               0               4
  STAGE IIA              1               5
  STAGE IIA1             1               4
  STAGE IIA2             1               6
  STAGE IIB              1              13
  STAGE III              1               0
  STAGE IIIB             3              26
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     8   3
  KRAS WILD-TYPE 142  39
  KRAS MUTATED KRAS WILD-TYPE 
            11            181 
  KRAS MUTATED KRAS WILD-TYPE 
             3             39 
$`KRAS MUTATED`
TCGA-C5-A1ME TCGA-C5-A2M1 TCGA-C5-A3HF TCGA-DG-A2KK TCGA-EA-A4BA TCGA-EK-A2R8 
       57.73        38.43        17.85        82.06        24.82         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RL TCGA-FU-A3EO TCGA-FU-A57G TCGA-JW-A5VH 
        0.13        47.77        16.11        35.44         3.29 

$`KRAS WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH 
       31.40        46.32        30.21        35.01        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        33.24        52.01        18.02        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
       17.19       155.77       131.11         9.34         1.12        95.11 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
      117.99       118.65        28.90        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.36        33.30        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 
       24.56        31.73        26.01        12.13         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.39         0.43         0.59         0.89        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RM 
        4.24         0.07         1.87         1.74         0.43         1.64 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
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-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       14.01        10.55         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
       12.49         0.30         0.82        13.35        28.08        34.62 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        35.05        20.84        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-WL-A834 
       26.01 

  KRAS MUTATED KRAS WILD-TYPE 
          0.13           0.07 
  KRAS MUTATED KRAS WILD-TYPE 
         82.06         210.67 
  KRAS MUTATED KRAS WILD-TYPE 
         24.82          23.67 
[1] "0.1 - 82.1 (24.8)"  "0.1 - 210.7 (23.7)"
[1] "hr=" "1.5"
D4V2, continuous
                vv
clus             T1 T2 T3+T4
  KRAS MUTATED    8  1     1
  KRAS WILD-TYPE 96 39     4
D4V3, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               8             96
  T2               1             39
  T3+T4            1              4
[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"
D4V4, binary
                cls
clus              0  1
  KRAS MUTATED    6  3
  KRAS WILD-TYPE 89 41
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    3
  KRAS WILD-TYPE   89   41
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            6             89
  1            3             41
[1] 2 2
[1] FALSE
D4V5, binary
                cls
clus              0  1
  KRAS MUTATED    3  1
  KRAS WILD-TYPE 76  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    1
  KRAS WILD-TYPE   76    3
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            3             76
  1            1              3
[1] 2 2
[1] FALSE
D4V6, binary
                cls
clus              0  1
  KRAS MUTATED    1  2
  KRAS WILD-TYPE 39 50
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    2
  KRAS WILD-TYPE   39   50
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             1             39
  YES            2             50
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  KRAS MUTATED               0                                4
  KRAS WILD-TYPE             4                              154
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  KRAS MUTATED                                               0
  KRAS WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  KRAS MUTATED                                     6
  KRAS WILD-TYPE                                  15
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  KRAS MUTATED                                           0
  KRAS WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  KRAS MUTATED                                              1
  KRAS WILD-TYPE                                            3
D4V7, multiclass
                                               clus
vv                                              KRAS MUTATED KRAS WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         4            154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      6             15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             1              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  1     0
  KRAS WILD-TYPE                                7    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  KRAS MUTATED                           1
  KRAS WILD-TYPE                        15
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRAS MUTATED                                           0     8
  KRAS WILD-TYPE                                         1   130
D4V10, multiclass
                                           clus
vv                                          KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              7
  ASIAN                                                0             19
  BLACK OR AFRICAN AMERICAN                            1             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            130
[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"
D4V11, binary
                cls
clus               0   1
  KRAS MUTATED     1   9
  KRAS WILD-TYPE  13 126
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    9
  KRAS WILD-TYPE   13  126
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            9            126
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                cls
clus               0   1
  KRAS MUTATED     6   5
  KRAS WILD-TYPE 133  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    5
  KRAS WILD-TYPE  133   40
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  TUMOR FREE            6            133
  WITH TUMOR            5             40
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  KRAS MUTATED    1  7  3  0  0
  KRAS WILD-TYPE 13 81 79  1  8
D4V14, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  G1            1             13
  G2            7             81
  G3            3             79
  G4            0              1
  GX            0              8
[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"
D4V15, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             27 
    TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-C5-A1BJ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BQ     TCGA-C5-A1MF     TCGA-C5-A1MH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A7CM     TCGA-C5-A7CO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-EK-A2RA     TCGA-FU-A2QG     TCGA-FU-A3WB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7     TCGA-IR-A3LB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D4V16, continuous
D4V17, continuous
D4V18, continuous
D4V19, binary
                cls
clus              0  1
  KRAS MUTATED    1  0
  KRAS WILD-TYPE 25  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    0
  KRAS WILD-TYPE   25    3
                         clus
vv                        KRAS MUTATED KRAS WILD-TYPE
  COMPLETED AS PLANNED               1             25
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D4V20, continuous
D4V21, continuous
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  KRAS MUTATED                                     0
  KRAS WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  KRAS MUTATED                                     0                       3
  KRAS WILD-TYPE                                   7                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  KRAS MUTATED                         0                       1
  KRAS WILD-TYPE                       1                       7
D4V26, multiclass
                                     clus
vv                                    KRAS MUTATED KRAS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            0              7
  OTHER LOCATION, SPECIFY                        3             27
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              7
[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)
  KRAS MUTATED                                               0
  KRAS WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  KRAS MUTATED                                                0
  KRAS WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  KRAS MUTATED                                                                                   2
  KRAS WILD-TYPE                                                                                58
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  KRAS MUTATED                                                                                              7
  KRAS WILD-TYPE                                                                                           81
D4V27, multiclass
                                                                                              clus
vv                                                                                             KRAS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                          0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                       2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            7
                                                                                              clus
vv                                                                                             KRAS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V28, binary
                cls
clus              0  1
  KRAS MUTATED    7  2
  KRAS WILD-TYPE 56 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      7    2
  KRAS WILD-TYPE   56   65
         clus
vv        KRAS MUTATED KRAS WILD-TYPE
  ABSENT             7             56
  PRESENT            2             65
[1] 2 2
[1] FALSE
D4V29, continuous
D4V30, continuous
D4V31, binary
                cls
clus              0  1
  KRAS MUTATED    1  1
  KRAS WILD-TYPE 38 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    1
  KRAS WILD-TYPE   38   85
                                          clus
vv                                         KRAS MUTATED KRAS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                1             38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            1             85
[1] 2 2
[1] FALSE
D4V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  KRAS MUTATED              0           4          1
  KRAS WILD-TYPE            8          39         45
D4V33, multiclass
              clus
vv             KRAS MUTATED KRAS WILD-TYPE
  CURRENT USER            0              8
  FORMER USER             4             39
  NEVER USED              1             45
[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"
D4V34, continuous
D4V35, binary
                cls
clus              0  1
  KRAS MUTATED    8  1
  KRAS WILD-TYPE 80 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      8    1
  KRAS WILD-TYPE   80   15
         clus
vv        KRAS MUTATED KRAS WILD-TYPE
  ABSENT             8             80
  PRESENT            1             15
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  KRAS MUTATED             2         1     0
  KRAS WILD-TYPE           2        52     1
D4V36, multiclass
             clus
vv            KRAS MUTATED KRAS WILD-TYPE
  CARBOPLATIN            2              2
  CISPLATIN              1             52
  OTHER                  0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V37, continuous
D4V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  KRAS MUTATED         0        0         0         0        1         3
  KRAS WILD-TYPE       4        1         1         1       27        50
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  KRAS MUTATED           4        0         0          0          0         1
  KRAS WILD-TYPE        25        4         6          5          7        13
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  KRAS MUTATED           0          1         0         1
  KRAS WILD-TYPE         1         28         2         4
D4V39, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              1             27
  STAGE IB1             3             50
  STAGE IB2             4             25
  STAGE II              0              4
  STAGE IIA             0              6
  STAGE IIA1            0              5
  STAGE IIA2            0              7
  STAGE IIB             1             13
  STAGE III             0              1
  STAGE IIIB            1             28
  STAGE IVA             0              2
  STAGE IVB             1              4
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MLL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    13   9
  MLL2 WILD-TYPE 137  33
  MLL2 MUTATED MLL2 WILD-TYPE 
            22            170 
  MLL2 MUTATED MLL2 WILD-TYPE 
             9             33 
$`MLL2 MUTATED`
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LZ TCGA-C5-A3HE 
       82.85        19.86        20.91        40.93       100.14        18.02 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-EA-A3HQ TCGA-EA-A439 TCGA-EA-A6QX TCGA-EK-A2RK 
       58.88        36.76        37.35        31.73        24.00         0.43 
TCGA-EX-A1H6 TCGA-HG-A2PA TCGA-IR-A3LB TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A5VL 
        7.92        25.41        66.81        36.36        20.48        15.58 
TCGA-LP-A5U2 TCGA-Q1-A5R2 TCGA-Q1-A73O TCGA-UC-A7PF 
        0.30        16.41        14.07        93.99 

$`MLL2 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
      177.04       173.29         5.46        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43         3.58        33.90        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        9.34         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       87.75        55.63       117.99       118.65        28.90        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
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-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01        12.13        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         1.64         2.33         0.07         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
        0.89        20.35        15.22        19.79        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        29.85        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
        3.29        24.56        21.44        28.37         8.28        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      209.59        44.61        20.91        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.35        28.08        34.62        54.81        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84        15.58        15.95         9.04        16.14        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-WL-A834 
       11.67        26.01 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.30           0.07 
  MLL2 MUTATED MLL2 WILD-TYPE 
        100.14         210.67 
  MLL2 MUTATED MLL2 WILD-TYPE 
        24.705         23.325 
[1] "0.3 - 100.1 (24.7)" "0.1 - 210.7 (23.3)"
[1] "hr=" "2.1"
D5V2, continuous
                vv
clus             T1 T2 T3+T4
  MLL2 MUTATED   11  5     0
  MLL2 WILD-TYPE 93 35     5
D5V3, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T1              11             93
  T2               5             35
  T3+T4            0              5
[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"
D5V4, binary
                cls
clus              0  1
  MLL2 MUTATED    9  5
  MLL2 WILD-TYPE 86 39
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      9    5
  MLL2 WILD-TYPE   86   39
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0            9             86
  1            5             39
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus              0  1
  MLL2 MUTATED   10  0
  MLL2 WILD-TYPE 69  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     10    0
  MLL2 WILD-TYPE   69    4
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           10             69
  1            0              4
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus              0  1
  MLL2 MUTATED    4  8
  MLL2 WILD-TYPE 36 44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      4    8
  MLL2 WILD-TYPE   36   44
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO             4             36
  YES            8             44
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  MLL2 MUTATED               0                               19
  MLL2 WILD-TYPE             4                              139
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  MLL2 MUTATED                                               1
  MLL2 WILD-TYPE                                             4
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  MLL2 MUTATED                                     2
  MLL2 WILD-TYPE                                  19
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  MLL2 MUTATED                                           0
  MLL2 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  MLL2 MUTATED                                              0
  MLL2 WILD-TYPE                                            4
D5V7, multiclass
                                               clus
vv                                              MLL2 MUTATED MLL2 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                        19            139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            1              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      2             19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  1     3
  MLL2 WILD-TYPE                                7    16
                vv
clus             BLACK OR AFRICAN AMERICAN
  MLL2 MUTATED                           2
  MLL2 WILD-TYPE                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL2 MUTATED                                           0    14
  MLL2 WILD-TYPE                                         1   124
D5V10, multiclass
                                           clus
vv                                          MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              7
  ASIAN                                                3             16
  BLACK OR AFRICAN AMERICAN                            2             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            124
[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"
D5V11, binary
                cls
clus               0   1
  MLL2 MUTATED     2  15
  MLL2 WILD-TYPE  12 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   15
  MLL2 WILD-TYPE   12  120
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             12
  NOT HISPANIC OR LATINO           15            120
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                cls
clus               0   1
  MLL2 MUTATED    14   5
  MLL2 WILD-TYPE 125  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     14    5
  MLL2 WILD-TYPE  125   40
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  TUMOR FREE           14            125
  WITH TUMOR            5             40
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  MLL2 MUTATED    2  9 10  0  1
  MLL2 WILD-TYPE 12 79 72  1  7
D5V14, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  G1            2             12
  G2            9             79
  G3           10             72
  G4            0              1
  GX            1              7
[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"
D5V15, continuous
[1] "Remove cluster labels:" "MLL2 MUTATED"          
clus
  MLL2 MUTATED MLL2 WILD-TYPE 
             2             27 
    TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-C5-A1BJ 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A7CM     TCGA-C5-A7CO 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-DG-A2KK     TCGA-DS-A3LQ     TCGA-EK-A2RA     TCGA-FU-A2QG 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
D5V16, continuous
D5V17, continuous
D5V18, continuous
D5V19, binary
                cls
clus              0  1
  MLL2 MUTATED    4  0
  MLL2 WILD-TYPE 22  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      4    0
  MLL2 WILD-TYPE   22    3
                         clus
vv                        MLL2 MUTATED MLL2 WILD-TYPE
  COMPLETED AS PLANNED               4             22
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D5V20, continuous
D5V21, continuous
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MLL2 MUTATED                                     0
  MLL2 WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MLL2 MUTATED                                     0                       2
  MLL2 WILD-TYPE                                   7                      28
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MLL2 MUTATED                         0                       3
  MLL2 WILD-TYPE                       1                       5
D5V26, multiclass
                                     clus
vv                                    MLL2 MUTATED MLL2 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            0              7
  OTHER LOCATION, SPECIFY                        2             28
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        3              5
[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)
  MLL2 MUTATED                                               0
  MLL2 WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  MLL2 MUTATED                                                1
  MLL2 WILD-TYPE                                              9
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  MLL2 MUTATED                                                                                  10
  MLL2 WILD-TYPE                                                                                50
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  MLL2 MUTATED                                                                                             10
  MLL2 WILD-TYPE                                                                                           78
D5V27, multiclass
                                                                                              clus
vv                                                                                             MLL2 MUTATED
  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)                      10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)           10
                                                                                              clus
vv                                                                                             MLL2 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V28, binary
                cls
clus              0  1
  MLL2 MUTATED    4 10
  MLL2 WILD-TYPE 59 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      4   10
  MLL2 WILD-TYPE   59   57
         clus
vv        MLL2 MUTATED MLL2 WILD-TYPE
  ABSENT             4             59
  PRESENT           10             57
[1] 2 2
[1] FALSE
D5V29, continuous
D5V30, continuous
D5V31, binary
                cls
clus              0  1
  MLL2 MUTATED    4 12
  MLL2 WILD-TYPE 35 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      4   12
  MLL2 WILD-TYPE   35   74
                                          clus
vv                                         MLL2 MUTATED MLL2 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                4             35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA           12             74
[1] 2 2
[1] FALSE
D5V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  MLL2 MUTATED              1           3          5
  MLL2 WILD-TYPE            7          40         41
D5V33, multiclass
              clus
vv             MLL2 MUTATED MLL2 WILD-TYPE
  CURRENT USER            1              7
  FORMER USER             3             40
  NEVER USED              5             41
[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"
D5V34, continuous
D5V35, binary
                cls
clus              0  1
  MLL2 MUTATED    8  5
  MLL2 WILD-TYPE 80 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      8    5
  MLL2 WILD-TYPE   80   11
         clus
vv        MLL2 MUTATED MLL2 WILD-TYPE
  ABSENT             8             80
  PRESENT            5             11
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  MLL2 MUTATED             0         8     0
  MLL2 WILD-TYPE           4        45     1
D5V36, multiclass
             clus
vv            MLL2 MUTATED MLL2 WILD-TYPE
  CARBOPLATIN            0              4
  CISPLATIN              8             45
  OTHER                  0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V37, continuous
[1] "Remove cluster labels:" "MLL2 MUTATED"          
clus
  MLL2 MUTATED MLL2 WILD-TYPE 
             2              8 
    TCGA-C5-A1BN     TCGA-C5-A1MH     TCGA-C5-A1MP     TCGA-EK-A2RO 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-JW-A852     TCGA-JX-A3Q8     TCGA-MU-A51Y 
"MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" "MLL2 WILD-TYPE" 
D5V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  MLL2 MUTATED         0        0         0         1        2         4
  MLL2 WILD-TYPE       4        1         1         0       26        49
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  MLL2 MUTATED           6        1         0          1          0         0
  MLL2 WILD-TYPE        23        3         6          4          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  MLL2 MUTATED           0          6         0         0
  MLL2 WILD-TYPE         1         23         2         5
D5V39, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             1              0
  STAGE IB              2             26
  STAGE IB1             4             49
  STAGE IB2             6             23
  STAGE II              1              3
  STAGE IIA             0              6
  STAGE IIA1            1              4
  STAGE IIA2            0              7
  STAGE IIB             0             14
  STAGE III             0              1
  STAGE IIIB            6             23
  STAGE IVA             0              2
  STAGE IVB             0              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    15   4
  FBXW7 WILD-TYPE 135  38
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             173 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              38 
$`FBXW7 MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1M9 TCGA-C5-A7CG TCGA-DG-A2KK TCGA-DS-A0VN TCGA-DS-A1OA 
      144.16        35.01       210.67        82.06       118.65        28.90 
TCGA-EA-A3HQ TCGA-EA-A3QE TCGA-EA-A50E TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2RL 
       37.35        25.02         7.46         0.43         0.89        47.77 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A2QG TCGA-FU-A57G TCGA-FU-A5XV TCGA-JW-A5VJ 
        0.49         0.89        19.04        35.44        10.55        21.44 
TCGA-Q1-A73O 
       14.07 

$`FBXW7 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74        36.56       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        30.21        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ 
        0.46         2.43        20.91        40.93         3.58        33.90 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
       17.19       155.77       131.11         9.34         1.12        95.11 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
       39.55        40.87        30.90        31.36        33.30        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82        14.89        26.79        25.91        27.29        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-A2PK TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51        19.27         0.39         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 
        0.43         1.64         2.33         0.07         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
        7.92        15.22        19.79        12.23        23.84        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       14.01         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       24.56        20.48        15.58        28.37         8.28        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      209.59        44.61        20.91        11.28         0.89        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-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       35.05        20.84        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59        14.60        11.67        93.99        26.01 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.43            0.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         210.67          209.59 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          25.02           23.67 
[1] "0.4 - 210.7 (25.0)" "0.1 - 209.6 (23.7)"
[1] "hr=" "1.2"
D6V2, continuous
                 vv
clus              T1 T2 T3+T4
  FBXW7 MUTATED   11  2     2
  FBXW7 WILD-TYPE 93 38     3
D6V3, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T1               11              93
  T2                2              38
  T3+T4             2               3
[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"
D6V4, binary
                 cls
clus               0  1
  FBXW7 MUTATED    7  7
  FBXW7 WILD-TYPE 88 37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      7    7
  FBXW7 WILD-TYPE   88   37
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             7              88
  1             7              37
[1] 2 2
[1] FALSE
D6V5, binary
                 cls
clus               0  1
  FBXW7 MUTATED    8  0
  FBXW7 WILD-TYPE 71  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      8    0
  FBXW7 WILD-TYPE   71    4
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             8              71
  1             0               4
[1] 2 2
[1] FALSE
D6V6, binary
                 cls
clus               0  1
  FBXW7 MUTATED    2  3
  FBXW7 WILD-TYPE 38 49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2    3
  FBXW7 WILD-TYPE   38   49
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              2              38
  YES             3              49
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  FBXW7 MUTATED               0                               15
  FBXW7 WILD-TYPE             4                              143
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  FBXW7 MUTATED                                               0
  FBXW7 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  FBXW7 MUTATED                                     4
  FBXW7 WILD-TYPE                                  17
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  FBXW7 MUTATED                                           0
  FBXW7 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  FBXW7 MUTATED                                              0
  FBXW7 WILD-TYPE                                            4
D6V7, multiclass
                                               clus
vv                                              FBXW7 MUTATED FBXW7 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                         15             143
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       4              17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  1     2
  FBXW7 WILD-TYPE                                7    17
                 vv
clus              BLACK OR AFRICAN AMERICAN
  FBXW7 MUTATED                           1
  FBXW7 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXW7 MUTATED                                           0    13
  FBXW7 WILD-TYPE                                         1   125
D6V10, multiclass
                                           clus
vv                                          FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               7
  ASIAN                                                 2              17
  BLACK OR AFRICAN AMERICAN                             1              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             125
[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"
D6V11, binary
                 cls
clus                0   1
  FBXW7 MUTATED     2  14
  FBXW7 WILD-TYPE  12 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2   14
  FBXW7 WILD-TYPE   12  121
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            14             121
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                 cls
clus                0   1
  FBXW7 MUTATED    12   7
  FBXW7 WILD-TYPE 127  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     12    7
  FBXW7 WILD-TYPE  127   38
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  TUMOR FREE            12             127
  WITH TUMOR             7              38
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  FBXW7 MUTATED    0  9  8  0  1
  FBXW7 WILD-TYPE 14 79 74  1  7
D6V14, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  G1             0              14
  G2             9              79
  G3             8              74
  G4             0               1
  GX             1               7
[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"
D6V15, continuous
D6V16, continuous
D6V17, continuous
D6V18, continuous
D6V19, binary
                 cls
clus               0  1
  FBXW7 MUTATED    2  0
  FBXW7 WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2    0
  FBXW7 WILD-TYPE   24    3
                         clus
vv                        FBXW7 MUTATED FBXW7 WILD-TYPE
  COMPLETED AS PLANNED                2              24
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D6V20, continuous
D6V21, continuous
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FBXW7 MUTATED                                     0
  FBXW7 WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FBXW7 MUTATED                                     0                       5
  FBXW7 WILD-TYPE                                   7                      25
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FBXW7 MUTATED                         1                       0
  FBXW7 WILD-TYPE                       0                       8
D6V26, multiclass
                                     clus
vv                                    FBXW7 MUTATED FBXW7 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             0               7
  OTHER LOCATION, SPECIFY                         5              25
  POSITIVE BLADDER MARGIN                         1               0
  POSITIVE VAGINAL MARGIN                         0               8
[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)
  FBXW7 MUTATED                                               0
  FBXW7 WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  FBXW7 MUTATED                                                1
  FBXW7 WILD-TYPE                                              9
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  FBXW7 MUTATED                                                                                   4
  FBXW7 WILD-TYPE                                                                                56
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  FBXW7 MUTATED                                                                                              9
  FBXW7 WILD-TYPE                                                                                           79
D6V27, multiclass
                                                                                              clus
vv                                                                                             FBXW7 MUTATED
  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)             9
                                                                                              clus
vv                                                                                             FBXW7 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V28, binary
                 cls
clus               0  1
  FBXW7 MUTATED    8  7
  FBXW7 WILD-TYPE 55 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      8    7
  FBXW7 WILD-TYPE   55   60
         clus
vv        FBXW7 MUTATED FBXW7 WILD-TYPE
  ABSENT              8              55
  PRESENT             7              60
[1] 2 2
[1] FALSE
D6V29, continuous
D6V30, continuous
D6V31, binary
                 cls
clus               0  1
  FBXW7 MUTATED    3  8
  FBXW7 WILD-TYPE 36 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      3    8
  FBXW7 WILD-TYPE   36   78
                                          clus
vv                                         FBXW7 MUTATED FBXW7 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 3              36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             8              78
[1] 2 2
[1] FALSE
D6V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  FBXW7 MUTATED              2           5          5
  FBXW7 WILD-TYPE            6          38         41
D6V33, multiclass
              clus
vv             FBXW7 MUTATED FBXW7 WILD-TYPE
  CURRENT USER             2               6
  FORMER USER              5              38
  NEVER USED               5              41
[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"
D6V34, continuous
D6V35, binary
                 cls
clus               0  1
  FBXW7 MUTATED   10  2
  FBXW7 WILD-TYPE 78 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     10    2
  FBXW7 WILD-TYPE   78   14
         clus
vv        FBXW7 MUTATED FBXW7 WILD-TYPE
  ABSENT             10              78
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  FBXW7 MUTATED             1         5     0
  FBXW7 WILD-TYPE           3        48     1
D6V36, multiclass
             clus
vv            FBXW7 MUTATED FBXW7 WILD-TYPE
  CARBOPLATIN             1               3
  CISPLATIN               5              48
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V37, continuous
D6V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  FBXW7 MUTATED         0        0         0         0        6         3
  FBXW7 WILD-TYPE       4        1         1         1       22        50
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  FBXW7 MUTATED           2        1         0          0          0         2
  FBXW7 WILD-TYPE        27        3         6          5          7        12
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  FBXW7 MUTATED           0          4         1         0
  FBXW7 WILD-TYPE         1         25         1         5
D6V39, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               6              22
  STAGE IB1              3              50
  STAGE IB2              2              27
  STAGE II               1               3
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              2              12
  STAGE III              0               1
  STAGE IIIB             4              25
  STAGE IVA              1               1
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = EP300 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    17   4
  EP300 WILD-TYPE 133  38
  EP300 MUTATED EP300 WILD-TYPE 
             21             171 
  EP300 MUTATED EP300 WILD-TYPE 
              4              38 
$`EP300 MUTATED`
TCGA-C5-A1MH TCGA-C5-A7CG TCGA-C5-A7UH TCGA-EA-A3HQ TCGA-EA-A3HU TCGA-EA-A3QD 
       38.99       210.67       131.11        37.35        33.30        13.05 
TCGA-EA-A5O9 TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2RK TCGA-EK-A3GK TCGA-EX-A1H5 
       25.91         0.59         1.45         0.43         0.49        20.35 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-IR-A3LK TCGA-JW-A852 TCGA-JX-A3Q0 
       31.36        20.98        26.14        29.85         8.28       209.59 
TCGA-LP-A5U2 TCGA-MY-A5BD TCGA-MY-A5BE 
        0.30        54.81        35.05 

$`EP300 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
      147.35        17.19       155.77         9.34         1.12        95.11 
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-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
       55.63       117.99       118.65        28.90        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       16.18        17.52         8.28        39.55        40.87        30.90 
TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       31.36        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       27.29        27.25        27.22        24.00        13.48        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.89         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        1.87         1.74        47.77         1.64         2.33         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K 
        0.10         0.89         7.92        15.22        19.79        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ 
       23.84        19.04        16.11        36.26        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
       14.01        35.44        10.55         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        44.61        20.91        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.82        13.35        28.08        34.62        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  EP300 MUTATED EP300 WILD-TYPE 
           0.30            0.07 
  EP300 MUTATED EP300 WILD-TYPE 
         210.67          177.04 
  EP300 MUTATED EP300 WILD-TYPE 
          26.14           22.98 
[1] "0.3 - 210.7 (26.1)" "0.1 - 177.0 (23.0)"
[1] "hr=" "1.2"
D7V2, continuous
                 vv
clus              T1 T2 T3+T4
  EP300 MUTATED   10  7     1
  EP300 WILD-TYPE 94 33     4
D7V3, multiclass
       clus
vv      EP300 MUTATED EP300 WILD-TYPE
  T1               10              94
  T2                7              33
  T3+T4             1               4
[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"
D7V4, binary
                 cls
clus               0  1
  EP300 MUTATED   10  8
  EP300 WILD-TYPE 85 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     10    8
  EP300 WILD-TYPE   85   36
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            10              85
  1             8              36
[1] 2 2
[1] FALSE
D7V5, binary
                 cls
clus               0  1
  EP300 MUTATED    7  0
  EP300 WILD-TYPE 72  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      7    0
  EP300 WILD-TYPE   72    4
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0             7              72
  1             0               4
[1] 2 2
[1] FALSE
D7V6, binary
                 cls
clus               0  1
  EP300 MUTATED    5  4
  EP300 WILD-TYPE 35 48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      5    4
  EP300 WILD-TYPE   35   48
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              5              35
  YES             4              48
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  EP300 MUTATED               0                               19
  EP300 WILD-TYPE             4                              139
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  EP300 MUTATED                                               1
  EP300 WILD-TYPE                                             4
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  EP300 MUTATED                                     1
  EP300 WILD-TYPE                                  20
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  EP300 MUTATED                                           0
  EP300 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  EP300 MUTATED                                              0
  EP300 WILD-TYPE                                            4
D7V7, multiclass
                                               clus
vv                                              EP300 MUTATED EP300 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                         19             139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             1               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       1              20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     1
  EP300 WILD-TYPE                                8    18
                 vv
clus              BLACK OR AFRICAN AMERICAN
  EP300 MUTATED                           3
  EP300 WILD-TYPE                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EP300 MUTATED                                           0    17
  EP300 WILD-TYPE                                         1   121
D7V10, multiclass
                                           clus
vv                                          EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 1              18
  BLACK OR AFRICAN AMERICAN                             3              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             121
[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"
D7V11, binary
                 cls
clus                0   1
  EP300 MUTATED     2  17
  EP300 WILD-TYPE  12 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   17
  EP300 WILD-TYPE   12  118
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            17             118
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                 cls
clus                0   1
  EP300 MUTATED    15   5
  EP300 WILD-TYPE 124  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     15    5
  EP300 WILD-TYPE  124   40
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  TUMOR FREE            15             124
  WITH TUMOR             5              40
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  EP300 MUTATED    1  9 11  0  0
  EP300 WILD-TYPE 13 79 71  1  8
D7V14, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  G1             1              13
  G2             9              79
  G3            11              71
  G4             0               1
  GX             0               8
[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"
D7V15, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              27 
     TCGA-EX-A69M      TCGA-FU-A3TX      TCGA-BI-A0VR      TCGA-C5-A1BJ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BQ      TCGA-C5-A1ME      TCGA-C5-A1MF 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A7CM      TCGA-C5-A7CO 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DS-A3LQ      TCGA-EK-A2RA      TCGA-FU-A2QG 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-MU-A5YI      TCGA-Q1-A6DW 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
D7V16, continuous
D7V17, continuous
D7V18, continuous
D7V19, binary
                 cls
clus               0  1
  EP300 MUTATED    2  0
  EP300 WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2    0
  EP300 WILD-TYPE   24    3
                         clus
vv                        EP300 MUTATED EP300 WILD-TYPE
  COMPLETED AS PLANNED                2              24
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D7V20, continuous
D7V21, continuous
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  EP300 MUTATED                                     0
  EP300 WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  EP300 MUTATED                                     2                       1
  EP300 WILD-TYPE                                   5                      29
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  EP300 MUTATED                         0                       1
  EP300 WILD-TYPE                       1                       7
D7V26, multiclass
                                     clus
vv                                    EP300 MUTATED EP300 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             2               5
  OTHER LOCATION, SPECIFY                         1              29
  POSITIVE BLADDER MARGIN                         0               1
  POSITIVE VAGINAL MARGIN                         1               7
[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)
  EP300 MUTATED                                               0
  EP300 WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  EP300 MUTATED                                                0
  EP300 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  EP300 MUTATED                                                                                  11
  EP300 WILD-TYPE                                                                                49
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  EP300 MUTATED                                                                                              7
  EP300 WILD-TYPE                                                                                           81
D7V27, multiclass
                                                                                              clus
vv                                                                                             EP300 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                       11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             7
                                                                                              clus
vv                                                                                             EP300 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V28, binary
                 cls
clus               0  1
  EP300 MUTATED    6  8
  EP300 WILD-TYPE 57 59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      6    8
  EP300 WILD-TYPE   57   59
         clus
vv        EP300 MUTATED EP300 WILD-TYPE
  ABSENT              6              57
  PRESENT             8              59
[1] 2 2
[1] FALSE
D7V29, continuous
D7V30, continuous
D7V31, binary
                 cls
clus               0  1
  EP300 MUTATED    6  9
  EP300 WILD-TYPE 33 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      6    9
  EP300 WILD-TYPE   33   77
                                          clus
vv                                         EP300 MUTATED EP300 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 6              33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             9              77
[1] 2 2
[1] FALSE
D7V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  EP300 MUTATED              1           3          8
  EP300 WILD-TYPE            7          40         38
D7V33, multiclass
              clus
vv             EP300 MUTATED EP300 WILD-TYPE
  CURRENT USER             1               7
  FORMER USER              3              40
  NEVER USED               8              38
[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"
D7V34, continuous
D7V35, binary
                 cls
clus               0  1
  EP300 MUTATED    8  2
  EP300 WILD-TYPE 80 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      8    2
  EP300 WILD-TYPE   80   14
         clus
vv        EP300 MUTATED EP300 WILD-TYPE
  ABSENT              8              80
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  EP300 MUTATED             0         3     0
  EP300 WILD-TYPE           4        50     1
D7V36, multiclass
             clus
vv            EP300 MUTATED EP300 WILD-TYPE
  CARBOPLATIN             0               4
  CISPLATIN               3              50
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V37, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2               8 
     TCGA-C5-A1BN      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-HM-A3JK      TCGA-JX-A3Q8      TCGA-MU-A51Y 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
D7V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  EP300 MUTATED         0        0         0         1        1         3
  EP300 WILD-TYPE       4        1         1         0       27        50
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  EP300 MUTATED           4        2         0          0          0         4
  EP300 WILD-TYPE        25        2         6          5          7        10
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  EP300 MUTATED           1          5         0         0
  EP300 WILD-TYPE         0         24         2         5
D7V39, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              1               0
  STAGE IB               1              27
  STAGE IB1              3              50
  STAGE IB2              4              25
  STAGE II               2               2
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              4              10
  STAGE III              1               0
  STAGE IIIB             5              24
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MAPK1 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  MAPK1 MUTATED     9   0
  MAPK1 WILD-TYPE 141  42
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             183 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              0              42 
$`MAPK1 MUTATED`
TCGA-C5-A1BI TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A5ZD 
       36.56        44.94       118.65        39.55        31.36        27.29 
TCGA-EK-A2RA TCGA-FU-A3TQ TCGA-HM-A3JK 
       40.96        26.14        20.78 

$`MAPK1 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        95.11        82.06        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63       117.99        28.90        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         8.28        40.87        37.35        30.90 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       33.30        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        25.91        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB 
        0.43         0.59         0.89         1.45         0.13         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.64         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
       20.35         7.92        15.22        19.79        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB 
       19.04        16.11        31.36        36.26        20.98        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       28.31        14.01        35.44        10.55         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       28.08        34.62        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  MAPK1 MUTATED MAPK1 WILD-TYPE 
          20.78            0.07 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
         118.65          210.67 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
          36.56           21.67 
[1] "20.8 - 118.7 (36.6)" "0.1 - 210.7 (21.7)" 
[1] "hr="     "2.7e+07"
D8V2, continuous
                 vv
clus               T1  T2 T3+T4
  MAPK1 MUTATED     4   4     0
  MAPK1 WILD-TYPE 100  36     5
D8V3, multiclass
       clus
vv      MAPK1 MUTATED MAPK1 WILD-TYPE
  T1                4             100
  T2                4              36
  T3+T4             0               5
[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"
D8V4, binary
                 cls
clus               0  1
  MAPK1 MUTATED    6  2
  MAPK1 WILD-TYPE 89 42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      6    2
  MAPK1 WILD-TYPE   89   42
   clus
vv  MAPK1 MUTATED MAPK1 WILD-TYPE
  0             6              89
  1             2              42
[1] 2 2
[1] FALSE
D8V5, binary
                 cls
clus               0  1
  MAPK1 MUTATED    5  0
  MAPK1 WILD-TYPE 74  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      5    0
  MAPK1 WILD-TYPE   74    4
   clus
vv  MAPK1 MUTATED MAPK1 WILD-TYPE
  0             5              74
  1             0               4
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus               0  1
  MAPK1 MUTATED    2  2
  MAPK1 WILD-TYPE 38 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      2    2
  MAPK1 WILD-TYPE   38   50
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  NO              2              38
  YES             2              50
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  MAPK1 MUTATED               0                                9
  MAPK1 WILD-TYPE             4                              149
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  MAPK1 MUTATED                                               0
  MAPK1 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  MAPK1 MUTATED                                     0
  MAPK1 WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  MAPK1 MUTATED                                           0
  MAPK1 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  MAPK1 MUTATED                                              0
  MAPK1 WILD-TYPE                                            4
D8V7, multiclass
                                               clus
vv                                              MAPK1 MUTATED MAPK1 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          9             149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK1 MUTATED                                  0     1
  MAPK1 WILD-TYPE                                8    18
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MAPK1 MUTATED                           0
  MAPK1 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAPK1 MUTATED                                           0     6
  MAPK1 WILD-TYPE                                         1   132
D8V10, multiclass
                                           clus
vv                                          MAPK1 MUTATED MAPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 1              18
  BLACK OR AFRICAN AMERICAN                             0              16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             132
[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"
D8V11, binary
                 cls
clus                0   1
  MAPK1 MUTATED     1   7
  MAPK1 WILD-TYPE  13 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      1    7
  MAPK1 WILD-TYPE   13  128
                        clus
vv                       MAPK1 MUTATED MAPK1 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             7             128
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                 cls
clus                0   1
  MAPK1 MUTATED     8   1
  MAPK1 WILD-TYPE 131  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      8    1
  MAPK1 WILD-TYPE  131   44
            clus
vv           MAPK1 MUTATED MAPK1 WILD-TYPE
  TUMOR FREE             8             131
  WITH TUMOR             1              44
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  MAPK1 MUTATED    2  5  2  0  0
  MAPK1 WILD-TYPE 12 83 80  1  8
D8V14, multiclass
    clus
vv   MAPK1 MUTATED MAPK1 WILD-TYPE
  G1             2              12
  G2             5              83
  G3             2              80
  G4             0               1
  GX             0               8
[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"
D8V15, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2              27 
     TCGA-EX-A69M      TCGA-FU-A3TX      TCGA-BI-A0VR      TCGA-C5-A1BJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BQ      TCGA-C5-A1ME      TCGA-C5-A1MF 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A7CM 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-DS-A3LQ      TCGA-FU-A2QG 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-HM-A4S6      TCGA-IR-A3L7      TCGA-IR-A3LB 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D8V16, continuous
D8V17, continuous
D8V18, continuous
D8V19, binary
                 cls
clus               0  1
  MAPK1 MUTATED    1  0
  MAPK1 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      1    0
  MAPK1 WILD-TYPE   25    3
                         clus
vv                        MAPK1 MUTATED MAPK1 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D8V20, continuous
D8V21, continuous
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MAPK1 MUTATED                                     0
  MAPK1 WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MAPK1 MUTATED                                     0                       1
  MAPK1 WILD-TYPE                                   7                      29
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MAPK1 MUTATED                         0                       1
  MAPK1 WILD-TYPE                       1                       7
D8V26, multiclass
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2              45 
     TCGA-EX-A449      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-DG-A2KK      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EK-A2RC      TCGA-EK-A2RK      TCGA-EK-A2RN 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-MU-A51Y      TCGA-UC-A7PD 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-WL-A834 
"MAPK1 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  MAPK1 MUTATED                                               0
  MAPK1 WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  MAPK1 MUTATED                                                0
  MAPK1 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  MAPK1 MUTATED                                                                                   5
  MAPK1 WILD-TYPE                                                                                55
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  MAPK1 MUTATED                                                                                              3
  MAPK1 WILD-TYPE                                                                                           85
D8V27, multiclass
                                                                                              clus
vv                                                                                             MAPK1 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             3
                                                                                              clus
vv                                                                                             MAPK1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V28, binary
                 cls
clus               0  1
  MAPK1 MUTATED    6  2
  MAPK1 WILD-TYPE 57 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      6    2
  MAPK1 WILD-TYPE   57   65
         clus
vv        MAPK1 MUTATED MAPK1 WILD-TYPE
  ABSENT              6              57
  PRESENT             2              65
[1] 2 2
[1] FALSE
D8V29, continuous
D8V30, continuous
D8V31, binary
                 cls
clus               0  1
  MAPK1 MUTATED    3  4
  MAPK1 WILD-TYPE 36 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    4
  MAPK1 WILD-TYPE   36   82
                                          clus
vv                                         MAPK1 MUTATED MAPK1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 3              36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             4              82
[1] 2 2
[1] FALSE
D8V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  MAPK1 MUTATED              0           2          3
  MAPK1 WILD-TYPE            8          41         43
D8V33, multiclass
              clus
vv             MAPK1 MUTATED MAPK1 WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              2              41
  NEVER USED               3              43
[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"
D8V34, continuous
D8V35, binary
                 cls
clus               0  1
  MAPK1 MUTATED    5  2
  MAPK1 WILD-TYPE 83 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      5    2
  MAPK1 WILD-TYPE   83   14
         clus
vv        MAPK1 MUTATED MAPK1 WILD-TYPE
  ABSENT              5              83
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  MAPK1 MUTATED             0         2     0
  MAPK1 WILD-TYPE           4        51     1
D8V36, multiclass
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2              56 
     TCGA-C5-A1BE      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M9 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KM 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VM      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EK-A2H0      TCGA-EK-A2H1      TCGA-HM-A3JJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-JW-A5VG 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852      TCGA-LP-A4AU 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73O 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-Q1-A73Q      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D8V37, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1               9 
     TCGA-C5-A1BN      TCGA-C5-A1MH      TCGA-C5-A1ML      TCGA-C5-A1MN 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-EK-A2RO      TCGA-JW-A852      TCGA-JX-A3Q8 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-MU-A51Y 
"MAPK1 WILD-TYPE" 
D8V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  MAPK1 MUTATED         0        0         0         0        2         2
  MAPK1 WILD-TYPE       4        1         1         1       26        51
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  MAPK1 MUTATED           0        0         1          0          2         0
  MAPK1 WILD-TYPE        29        4         5          5          5        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  MAPK1 MUTATED           0          2         0         0
  MAPK1 WILD-TYPE         1         27         2         5
D8V39, multiclass
            clus
vv           MAPK1 MUTATED MAPK1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               2              26
  STAGE IB1              2              51
  STAGE IB2              0              29
  STAGE II               0               4
  STAGE IIA              1               5
  STAGE IIA1             0               5
  STAGE IIA2             2               5
  STAGE IIB              0              14
  STAGE III              0               1
  STAGE IIIB             2              27
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MLL3 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    24   4
  MLL3 WILD-TYPE 126  38
  MLL3 MUTATED MLL3 WILD-TYPE 
            28            164 
  MLL3 MUTATED MLL3 WILD-TYPE 
             4             38 
$`MLL3 MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BQ TCGA-C5-A2LZ TCGA-C5-A3HL 
       57.04       144.16       173.29        19.86       100.14        20.42 
TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UH TCGA-DG-A2KK TCGA-DR-A0ZM TCGA-DS-A0VM 
      154.32       147.35       131.11        82.06        58.88       117.99 
TCGA-EK-A2PG TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.51         4.24         0.07         0.43         0.10         0.49 
TCGA-EX-A1H6 TCGA-FU-A770 TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JX-A3Q0 TCGA-MU-A51Y 
        7.92         1.12        29.85        15.58       209.59        28.08 
TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-UC-A7PF 
       16.41        17.56        14.07        93.99 

$`MLL3 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A20A 
       12.59        14.70         8.32         1.48        49.48        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM 
       11.44        68.84        18.74        36.56       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT 
       20.91        40.93         3.58        33.90        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
       20.35        17.19       155.77         9.34         1.12        95.11 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
       44.94        63.98        87.75        36.76        55.63       118.65 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       28.90        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU 
       39.55        40.87        37.35        30.90        31.36        33.30 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72        26.27         6.64        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        1.87         1.74        47.77         1.64         2.33         0.07 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
        0.89        20.35        15.22        19.79        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA 
       16.14        28.31        14.01        35.44        10.55        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL 
       66.81       129.37        96.95        78.71        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        20.48        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        8.28        21.11        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MY-A5BD 
       12.49         0.30         0.82        13.35        34.62        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       35.05        20.84        15.58        15.95         9.04        16.14 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-WL-A834 
       11.67        26.01 

  MLL3 MUTATED MLL3 WILD-TYPE 
          0.07           0.07 
  MLL3 MUTATED MLL3 WILD-TYPE 
        209.59         210.67 
  MLL3 MUTATED MLL3 WILD-TYPE 
        24.250         23.755 
[1] "0.1 - 209.6 (24.2)" "0.1 - 210.7 (23.8)"
[1] "hr=" "2.6"
D9V2, continuous
                vv
clus             T1 T2 T3+T4
  MLL3 MUTATED   12  3     1
  MLL3 WILD-TYPE 92 37     4
D9V3, multiclass
       clus
vv      MLL3 MUTATED MLL3 WILD-TYPE
  T1              12             92
  T2               3             37
  T3+T4            1              4
[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"
D9V4, binary
                cls
clus              0  1
  MLL3 MUTATED   11  4
  MLL3 WILD-TYPE 84 40
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     11    4
  MLL3 WILD-TYPE   84   40
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           11             84
  1            4             40
[1] 2 2
[1] FALSE
D9V5, binary
                cls
clus              0  1
  MLL3 MUTATED    7  0
  MLL3 WILD-TYPE 72  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      7    0
  MLL3 WILD-TYPE   72    4
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0            7             72
  1            0              4
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus              0  1
  MLL3 MUTATED    4 10
  MLL3 WILD-TYPE 36 42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      4   10
  MLL3 WILD-TYPE   36   42
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO             4             36
  YES           10             42
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  MLL3 MUTATED               0                               25
  MLL3 WILD-TYPE             4                              133
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  MLL3 MUTATED                                               1
  MLL3 WILD-TYPE                                             4
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  MLL3 MUTATED                                     3
  MLL3 WILD-TYPE                                  18
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  MLL3 MUTATED                                           0
  MLL3 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  MLL3 MUTATED                                              0
  MLL3 WILD-TYPE                                            4
D9V7, multiclass
                                               clus
vv                                              MLL3 MUTATED MLL3 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                        25            133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            1              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      3             18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  2     0
  MLL3 WILD-TYPE                                6    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  MLL3 MUTATED                           2
  MLL3 WILD-TYPE                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL3 MUTATED                                           1    20
  MLL3 WILD-TYPE                                         0   118
D9V10, multiclass
                                           clus
vv                                          MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     2              6
  ASIAN                                                0             19
  BLACK OR AFRICAN AMERICAN                            2             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               20            118
[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"
D9V11, binary
                cls
clus               0   1
  MLL3 MUTATED     3  17
  MLL3 WILD-TYPE  11 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      3   17
  MLL3 WILD-TYPE   11  118
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                3             11
  NOT HISPANIC OR LATINO           17            118
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                cls
clus               0   1
  MLL3 MUTATED    22   2
  MLL3 WILD-TYPE 117  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     22    2
  MLL3 WILD-TYPE  117   43
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  TUMOR FREE           22            117
  WITH TUMOR            2             43
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  MLL3 MUTATED    2 14 11  0  2
  MLL3 WILD-TYPE 12 74 71  1  6
D9V14, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  G1            2             12
  G2           14             74
  G3           11             71
  G4            0              1
  GX            2              6
[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"
D9V15, continuous
D9V16, continuous
D9V17, continuous
D9V18, continuous
D9V19, binary
                cls
clus              0  1
  MLL3 MUTATED    4  0
  MLL3 WILD-TYPE 22  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      4    0
  MLL3 WILD-TYPE   22    3
                         clus
vv                        MLL3 MUTATED MLL3 WILD-TYPE
  COMPLETED AS PLANNED               4             22
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D9V20, continuous
D9V21, continuous
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MLL3 MUTATED                                     0
  MLL3 WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MLL3 MUTATED                                     1                       5
  MLL3 WILD-TYPE                                   6                      25
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MLL3 MUTATED                         0                       2
  MLL3 WILD-TYPE                       1                       6
D9V26, multiclass
                                     clus
vv                                    MLL3 MUTATED MLL3 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            1              6
  OTHER LOCATION, SPECIFY                        5             25
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        2              6
[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)
  MLL3 MUTATED                                               0
  MLL3 WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  MLL3 MUTATED                                                0
  MLL3 WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  MLL3 MUTATED                                                                                  14
  MLL3 WILD-TYPE                                                                                46
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  MLL3 MUTATED                                                                                             10
  MLL3 WILD-TYPE                                                                                           78
D9V27, multiclass
                                                                                              clus
vv                                                                                             MLL3 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                          0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                      14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)           10
                                                                                              clus
vv                                                                                             MLL3 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V28, binary
                cls
clus              0  1
  MLL3 MUTATED   10  7
  MLL3 WILD-TYPE 53 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     10    7
  MLL3 WILD-TYPE   53   60
         clus
vv        MLL3 MUTATED MLL3 WILD-TYPE
  ABSENT            10             53
  PRESENT            7             60
[1] 2 2
[1] FALSE
D9V29, continuous
D9V30, continuous
D9V31, binary
                cls
clus              0  1
  MLL3 MUTATED    6 11
  MLL3 WILD-TYPE 33 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      6   11
  MLL3 WILD-TYPE   33   75
                                          clus
vv                                         MLL3 MUTATED MLL3 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                6             33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA           11             75
[1] 2 2
[1] FALSE
D9V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  MLL3 MUTATED              2           5          4
  MLL3 WILD-TYPE            6          38         42
D9V33, multiclass
              clus
vv             MLL3 MUTATED MLL3 WILD-TYPE
  CURRENT USER            2              6
  FORMER USER             5             38
  NEVER USED              4             42
[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"
D9V34, continuous
D9V35, binary
                cls
clus              0  1
  MLL3 MUTATED   12  2
  MLL3 WILD-TYPE 76 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     12    2
  MLL3 WILD-TYPE   76   14
         clus
vv        MLL3 MUTATED MLL3 WILD-TYPE
  ABSENT            12             76
  PRESENT            2             14
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  MLL3 MUTATED             0        10     0
  MLL3 WILD-TYPE           4        43     1
D9V36, multiclass
             clus
vv            MLL3 MUTATED MLL3 WILD-TYPE
  CARBOPLATIN            0              4
  CISPLATIN             10             43
  OTHER                  0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V37, continuous
[1] "Remove cluster labels:" "MLL3 MUTATED"          
clus
  MLL3 MUTATED MLL3 WILD-TYPE 
             1              9 
    TCGA-C5-A1BN     TCGA-C5-A1MH     TCGA-C5-A1ML     TCGA-C5-A1MN 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-EK-A2RO     TCGA-HM-A3JK     TCGA-JW-A852 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-JX-A3Q8 
"MLL3 WILD-TYPE" 
D9V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  MLL3 MUTATED         1        0         0         1        3         6
  MLL3 WILD-TYPE       3        1         1         0       25        47
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  MLL3 MUTATED           5        0         1          1          0         2
  MLL3 WILD-TYPE        24        4         5          4          7        12
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  MLL3 MUTATED           1          6         0         0
  MLL3 WILD-TYPE         0         23         2         5
D9V39, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               1              3
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             1              0
  STAGE IB              3             25
  STAGE IB1             6             47
  STAGE IB2             5             24
  STAGE II              0              4
  STAGE IIA             1              5
  STAGE IIA1            1              4
  STAGE IIA2            0              7
  STAGE IIB             2             12
  STAGE III             1              0
  STAGE IIIB            6             23
  STAGE IVA             0              2
  STAGE IVB             0              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = ARID1A MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     9   4
  ARID1A WILD-TYPE 141  38
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              179 
  ARID1A MUTATED ARID1A WILD-TYPE 
               4               38 
$`ARID1A MUTATED`
TCGA-EX-A449 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MK TCGA-DS-A7WH TCGA-EA-A4BA 
       14.70        35.01        35.61         2.43        17.52        24.82 
TCGA-FU-A3HZ TCGA-FU-A57G TCGA-IR-A3LA TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JX-A3Q0 
       36.26        35.44       137.16         3.29        15.58       209.59 
TCGA-Q1-A73O 
       14.07 

$`ARID1A WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A 
       12.59         8.32         1.48        49.48        57.04        23.67 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       11.44        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       46.32        30.21        57.73        53.16        38.99         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT 
       20.91        40.93         3.58        33.90        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
      155.77       131.11         9.34         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
      117.99       118.65        28.90        22.98        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
        8.28        39.55        40.87        37.35        30.90        31.36 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       33.30        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       31.73        26.01        12.13         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.89         1.45         0.13        40.96 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK 
        0.30         4.24         0.07         1.87         1.74         0.43 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         1.64         2.33         0.07         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K 
        0.89        20.35         7.92        15.22        19.79        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84        19.04        16.11        31.36        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       16.14        28.31        14.01        10.55         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       21.67        20.78        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       27.42        24.56        21.44        20.48        28.37         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        44.61        20.91        11.28         0.89        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-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       35.05        20.84        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59        14.60        11.67        93.99        26.01 

  ARID1A MUTATED ARID1A WILD-TYPE 
            2.43             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          209.59           210.67 
  ARID1A MUTATED ARID1A WILD-TYPE 
           24.82            23.67 
[1] "2.4 - 209.6 (24.8)" "0.1 - 210.7 (23.7)"
[1] "hr=" "1.3"
D10V2, continuous
                  vv
clus               T1 T2 T3+T4
  ARID1A MUTATED    7  1     3
  ARID1A WILD-TYPE 97 39     2
D10V3, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1                 7               97
  T2                 1               39
  T3+T4              3                2
[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"
D10V4, binary
                  cls
clus                0  1
  ARID1A MUTATED    6  2
  ARID1A WILD-TYPE 89 42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    2
  ARID1A WILD-TYPE   89   42
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              6               89
  1              2               42
[1] 2 2
[1] FALSE
D10V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    6  2
  ARID1A WILD-TYPE 73  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    2
  ARID1A WILD-TYPE   73    2
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              6               73
  1              2                2
[1] 2 2
[1] FALSE
D10V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  5
  ARID1A WILD-TYPE 38 47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   38   47
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               2               38
  YES              5               47
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ARID1A MUTATED               0                                7
  ARID1A WILD-TYPE             4                              151
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             5
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  ARID1A MUTATED                                     5
  ARID1A WILD-TYPE                                  16
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  ARID1A MUTATED                                           1
  ARID1A WILD-TYPE                                         1
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  ARID1A MUTATED                                              1
  ARID1A WILD-TYPE                                            3
D10V7, multiclass
                                               clus
vv                                              ARID1A MUTATED ARID1A WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           7              151
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              0                5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        5               16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  1                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               1                3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BL       TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1ML 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DR-A0ZM       TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A770       TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D10V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  2     0
  ARID1A WILD-TYPE                                6    19
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ARID1A MUTATED                           1
  ARID1A WILD-TYPE                        15
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1A MUTATED                                           0    10
  ARID1A WILD-TYPE                                         1   128
D10V10, multiclass
                                           clus
vv                                          ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       2                6
  ASIAN                                                  0               19
  BLACK OR AFRICAN AMERICAN                              1               15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              128
[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"
D10V11, binary
                  cls
clus                 0   1
  ARID1A MUTATED     4   9
  ARID1A WILD-TYPE  10 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    9
  ARID1A WILD-TYPE   10  126
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  4               10
  NOT HISPANIC OR LATINO              9              126
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                  cls
clus                 0   1
  ARID1A MUTATED     9   4
  ARID1A WILD-TYPE 130  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      9    4
  ARID1A WILD-TYPE  130   41
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  TUMOR FREE              9              130
  WITH TUMOR              4               41
[1] 2 2
[1] FALSE
                  vv
clus               G1 G2 G3 G4 GX
  ARID1A MUTATED    2  7  4  0  1
  ARID1A WILD-TYPE 12 81 78  1  7
D10V14, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  G1              2               12
  G2              7               81
  G3              4               78
  G4              0                1
  GX              1                7
[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"
D10V15, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               28 
      TCGA-EX-A69M       TCGA-FU-A3TX       TCGA-BI-A0VR       TCGA-C5-A1BJ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BL       TCGA-C5-A1BQ       TCGA-C5-A1ME       TCGA-C5-A1MF 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A2M2       TCGA-C5-A3HD       TCGA-C5-A7CM 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-DG-A2KK       TCGA-DS-A3LQ       TCGA-EK-A2RA 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3WB       TCGA-HM-A3JK       TCGA-HM-A4S6 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3L7       TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-MU-A5YI 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D10V16, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BL       TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1ML 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DR-A0ZM       TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A770       TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D10V17, continuous
D10V18, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               50 
      TCGA-FU-A3TX       TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BL       TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A2LS       TCGA-C5-A2LT 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DR-A0ZM 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-EA-A556       TCGA-EK-A2RA       TCGA-EX-A1H5 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-MU-A5YI 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S       TCGA-RA-A741 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D10V19, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  1
  ARID1A WILD-TYPE 24  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    1
  ARID1A WILD-TYPE   24    2
                         clus
vv                        ARID1A MUTATED ARID1A WILD-TYPE
  COMPLETED AS PLANNED                 2               24
  TREATMENT NOT COMPLETED              1                2
[1] 2 2
[1] FALSE
D10V20, continuous
D10V21, continuous
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ARID1A MUTATED                                     1
  ARID1A WILD-TYPE                                   0
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ARID1A MUTATED                                     0                       1
  ARID1A WILD-TYPE                                   7                      29
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ARID1A MUTATED                         0                       0
  ARID1A WILD-TYPE                       1                       8
D10V26, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               45 
      TCGA-BI-A20A       TCGA-C5-A0TN       TCGA-C5-A1BE       TCGA-C5-A1BK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MJ       TCGA-C5-A1MP 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1MQ       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2M1       TCGA-C5-A3HE       TCGA-C5-A3HL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CG       TCGA-C5-A7CJ       TCGA-C5-A7UC       TCGA-DG-A2KK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DG-A2KL       TCGA-DR-A0ZM       TCGA-DS-A0VK       TCGA-DS-A0VL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EA-A50E       TCGA-EK-A2RC       TCGA-EK-A2RK       TCGA-EK-A2RN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A3EO       TCGA-HM-A4S6       TCGA-IR-A3LH 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3LI       TCGA-IR-A3LK       TCGA-MU-A51Y       TCGA-UC-A7PD 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-WL-A834 
"ARID1A WILD-TYPE" 
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             3
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  ARID1A MUTATED                                                1
  ARID1A WILD-TYPE                                              9
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  ARID1A MUTATED                                                                                   5
  ARID1A WILD-TYPE                                                                                55
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ARID1A MUTATED                                                                                              8
  ARID1A WILD-TYPE                                                                                           80
D10V27, multiclass
                                                                                              clus
vv                                                                                             ARID1A MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              8
                                                                                              clus
vv                                                                                             ARID1A WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V28, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  4
  ARID1A WILD-TYPE 58 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    4
  ARID1A WILD-TYPE   58   63
         clus
vv        ARID1A MUTATED ARID1A WILD-TYPE
  ABSENT               5               58
  PRESENT              4               63
[1] 2 2
[1] FALSE
D10V29, continuous
D10V30, continuous
D10V31, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  5
  ARID1A WILD-TYPE 37 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   37   81
                                          clus
vv                                         ARID1A MUTATED ARID1A WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  2               37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              5               81
[1] 2 2
[1] FALSE
D10V32, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  ARID1A MUTATED              0           3          3
  ARID1A WILD-TYPE            8          40         43
D10V33, multiclass
              clus
vv             ARID1A MUTATED ARID1A WILD-TYPE
  CURRENT USER              0                8
  FORMER USER               3               40
  NEVER USED                3               43
[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"
D10V34, continuous
D10V35, binary
                  cls
clus                0  1
  ARID1A MUTATED    8  1
  ARID1A WILD-TYPE 80 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8    1
  ARID1A WILD-TYPE   80   15
         clus
vv        ARID1A MUTATED ARID1A WILD-TYPE
  ABSENT               8               80
  PRESENT              1               15
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  ARID1A MUTATED             3         6     0
  ARID1A WILD-TYPE           1        47     1
D10V36, multiclass
             clus
vv            ARID1A MUTATED ARID1A WILD-TYPE
  CARBOPLATIN              3                1
  CISPLATIN                6               47
  OTHER                    0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V37, continuous
D10V38, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  ARID1A MUTATED         0        0         0         0        0         4
  ARID1A WILD-TYPE       4        1         1         1       28        49
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  ARID1A MUTATED           4        0         1          0          1         0
  ARID1A WILD-TYPE        25        4         5          5          6        14
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  ARID1A MUTATED           1          1         0         2
  ARID1A WILD-TYPE         0         28         2         3
D10V39, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                0               28
  STAGE IB1               4               49
  STAGE IB2               4               25
  STAGE II                0                4
  STAGE IIA               1                5
  STAGE IIA1              0                5
  STAGE IIA2              1                6
  STAGE IIB               0               14
  STAGE III               1                0
  STAGE IIIB              1               28
  STAGE IVA               0                2
  STAGE IVB               2                3
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = NFE2L2 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     7   5
  NFE2L2 WILD-TYPE 143  37
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              180 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               5               37 
$`NFE2L2 MUTATED`
TCGA-C5-A1BL TCGA-C5-A1MH TCGA-C5-A1MN TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
      173.29        38.99        40.93        58.88        36.76       117.99 
TCGA-EK-A2PI TCGA-HG-A2PA TCGA-IR-A3LH TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3Q0 
       19.27        25.41        78.71        15.58         8.28       209.59 

$`NFE2L2 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       46.32        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS 
        0.46         2.43        20.91         3.58        33.90        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
       17.19       155.77       131.11         9.34         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN 
       82.06        44.94        63.98        87.75        55.63       118.65 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       28.90        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU 
       39.55        40.87        37.35        30.90        31.36        33.30 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.13        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72        26.27         6.64         1.51         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        1.64         2.33         0.07         0.10         0.49         0.89 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L 
       20.35         7.92        15.22        19.79        12.23        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       129.37        96.95        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        20.48        28.37 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        44.61        20.91        11.28         0.89        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-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       35.05        20.84        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       22.62        19.59        14.60        11.67        93.99        26.01 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            8.28             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          209.59           210.67 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          39.960           22.145 
[1] "8.3 - 209.6 (40.0)" "0.1 - 210.7 (22.1)"
[1] "hr=" "1.2"
D11V2, continuous
                  vv
clus                T1  T2 T3+T4
  NFE2L2 MUTATED     4   3     1
  NFE2L2 WILD-TYPE 100  37     4
D11V3, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1                 4              100
  T2                 3               37
  T3+T4              1                4
[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"
D11V4, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  3
  NFE2L2 WILD-TYPE 91 41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    3
  NFE2L2 WILD-TYPE   91   41
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              4               91
  1              3               41
[1] 2 2
[1] FALSE
D11V5, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    6  0
  NFE2L2 WILD-TYPE 73  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      6    0
  NFE2L2 WILD-TYPE   73    4
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              6               73
  1              0                4
[1] 2 2
[1] FALSE
D11V6, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  2
  NFE2L2 WILD-TYPE 36 50
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    2
  NFE2L2 WILD-TYPE   36   50
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               4               36
  YES              2               50
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED               0                               12
  NFE2L2 WILD-TYPE             4                              146
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                             5
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  NFE2L2 MUTATED                                     0
  NFE2L2 WILD-TYPE                                  21
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  NFE2L2 MUTATED                                           0
  NFE2L2 WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  NFE2L2 MUTATED                                              0
  NFE2L2 WILD-TYPE                                            4
D11V7, multiclass
                                               clus
vv                                              NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                          12              146
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              0                5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        0               21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
D11V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  1     0
  NFE2L2 WILD-TYPE                                7    19
                  vv
clus               BLACK OR AFRICAN AMERICAN
  NFE2L2 MUTATED                           2
  NFE2L2 WILD-TYPE                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L2 MUTATED                                           0     9
  NFE2L2 WILD-TYPE                                         1   129
D11V10, multiclass
                                           clus
vv                                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                7
  ASIAN                                                  0               19
  BLACK OR AFRICAN AMERICAN                              2               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              129
[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"
D11V11, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2   8
  NFE2L2 WILD-TYPE  12 127
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2    8
  NFE2L2 WILD-TYPE   12  127
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  2               12
  NOT HISPANIC OR LATINO              8              127
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     7   5
  NFE2L2 WILD-TYPE 132  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      7    5
  NFE2L2 WILD-TYPE  132   40
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  TUMOR FREE              7              132
  WITH TUMOR              5               40
[1] 2 2
[1] FALSE
                  vv
clus               G1 G2 G3 G4 GX
  NFE2L2 MUTATED    1  7  3  1  0
  NFE2L2 WILD-TYPE 13 81 79  0  8
D11V14, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  G1              1               13
  G2              7               81
  G3              3               79
  G4              1                0
  GX              0                8
[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"
D11V15, continuous
D11V16, continuous
D11V17, continuous
D11V18, continuous
D11V19, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  0
  NFE2L2 WILD-TYPE 22  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    0
  NFE2L2 WILD-TYPE   22    3
                         clus
vv                        NFE2L2 MUTATED NFE2L2 WILD-TYPE
  COMPLETED AS PLANNED                 4               22
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
D11V20, continuous
D11V21, continuous
D11V22, continuous
D11V23, continuous
D11V24, continuous
D11V25, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  NFE2L2 MUTATED                                     0
  NFE2L2 WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  NFE2L2 MUTATED                                     0                       2
  NFE2L2 WILD-TYPE                                   7                      28
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  NFE2L2 MUTATED                         0                       2
  NFE2L2 WILD-TYPE                       1                       6
D11V26, multiclass
                                     clus
vv                                    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              0                1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              0                7
  OTHER LOCATION, SPECIFY                          2               28
  POSITIVE BLADDER MARGIN                          0                1
  POSITIVE VAGINAL MARGIN                          2                6
[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)
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                             3
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  NFE2L2 MUTATED                                                0
  NFE2L2 WILD-TYPE                                             10
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  NFE2L2 MUTATED                                                                                   4
  NFE2L2 WILD-TYPE                                                                                56
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  NFE2L2 MUTATED                                                                                              7
  NFE2L2 WILD-TYPE                                                                                           81
D11V27, multiclass
                                                                                              clus
vv                                                                                             NFE2L2 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              7
                                                                                              clus
vv                                                                                             NFE2L2 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V28, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    1  5
  NFE2L2 WILD-TYPE 62 62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      1    5
  NFE2L2 WILD-TYPE   62   62
         clus
vv        NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ABSENT               1               62
  PRESENT              5               62
[1] 2 2
[1] FALSE
D11V29, continuous
D11V30, continuous
D11V31, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  6
  NFE2L2 WILD-TYPE 35 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    6
  NFE2L2 WILD-TYPE   35   80
                                          clus
vv                                         NFE2L2 MUTATED NFE2L2 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  4               35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              6               80
[1] 2 2
[1] FALSE
D11V32, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  NFE2L2 MUTATED              0           4          3
  NFE2L2 WILD-TYPE            8          39         43
D11V33, multiclass
              clus
vv             NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CURRENT USER              0                8
  FORMER USER               4               39
  NEVER USED                3               43
[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"
D11V34, continuous
D11V35, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  2
  NFE2L2 WILD-TYPE 84 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    2
  NFE2L2 WILD-TYPE   84   14
         clus
vv        NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ABSENT               4               84
  PRESENT              2               14
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  NFE2L2 MUTATED             0         6     0
  NFE2L2 WILD-TYPE           4        47     1
D11V36, multiclass
             clus
vv            NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CARBOPLATIN              0                4
  CISPLATIN                6               47
  OTHER                    0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V37, continuous
D11V38, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  NFE2L2 MUTATED         0        0         0         0        3         0
  NFE2L2 WILD-TYPE       4        1         1         1       25        53
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  NFE2L2 MUTATED           2        0         0          1          0         1
  NFE2L2 WILD-TYPE        27        4         6          4          7        13
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  NFE2L2 MUTATED           1          4         0         0
  NFE2L2 WILD-TYPE         0         25         2         5
D11V39, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                3               25
  STAGE IB1               0               53
  STAGE IB2               2               27
  STAGE II                0                4
  STAGE IIA               0                6
  STAGE IIA1              1                4
  STAGE IIA2              0                7
  STAGE IIB               1               13
  STAGE III               1                0
  STAGE IIIB              4               25
  STAGE IVA               0                2
  STAGE IVB               0                5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = PIK3CA MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    38  13
  PIK3CA WILD-TYPE 112  29
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              51              141 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              13               29 
$`PIK3CA MUTATED`
TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1MH TCGA-C5-A1MK 
       68.84       144.16        82.85        19.86        38.99         2.43 
TCGA-C5-A1ML TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7UH 
       20.91        38.43        18.02       101.82       147.35       131.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A3HT TCGA-EA-A3QE 
       82.06        44.94        16.83        16.18        31.36        25.02 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RD 
       24.82         7.46        26.79         1.51         0.59         0.07 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-FU-A23K TCGA-FU-A3HY TCGA-FU-A3HZ 
        2.33         0.07         0.10        12.23        31.36        36.26 
TCGA-FU-A3WB TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
       16.14        35.44        25.41        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       29.85         3.29        21.44        15.58        28.37         8.28 
TCGA-JX-A3Q0 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-MY-A5BE TCGA-Q1-A5R1 TCGA-Q1-A5R3 
      209.59        13.35        54.81        35.05        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-R2-A69V 
       16.14        15.88        19.59 

$`PIK3CA WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL 
       23.67        11.44        18.74        36.56       177.04       173.29 
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP 
       57.73        53.16        35.61         0.46        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        33.24        52.01        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      154.32       134.33        15.48        20.35        17.19       155.77 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        9.34         1.12        95.11        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76        55.63       117.99       118.65        28.90        22.98 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       33.30        13.05        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       26.01        12.13        14.89        25.91        27.29        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-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK 
       40.96         0.30         4.24         1.87         1.74         0.43 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
       47.77         1.64         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3NI 
       15.22        19.79        23.84        19.04        16.11        20.98 
TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ 
       26.14        28.31        14.01        10.55         1.12        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JX-A3PZ 
      129.37        36.36        27.42        24.56        20.48        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       44.61        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.82        28.08        34.62        20.84        16.41         9.04 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       17.56        14.07         9.34        18.64        22.62        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.07             0.13 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          209.59           210.67 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           24.82            23.67 
[1] "0.1 - 209.6 (24.8)" "0.1 - 210.7 (23.7)"
[1] "hr=" "1.2"
D12V2, continuous
                  vv
clus               T1 T2 T3+T4
  PIK3CA MUTATED   26 12     3
  PIK3CA WILD-TYPE 78 28     2
D12V3, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T1                26               78
  T2                12               28
  T3+T4              3                2
[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"
D12V4, binary
                  cls
clus                0  1
  PIK3CA MUTATED   27 10
  PIK3CA WILD-TYPE 68 34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     27   10
  PIK3CA WILD-TYPE   68   34
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             27               68
  1             10               34
[1] 2 2
[1] FALSE
D12V5, binary
                  cls
clus                0  1
  PIK3CA MUTATED   19  2
  PIK3CA WILD-TYPE 60  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     19    2
  PIK3CA WILD-TYPE   60    2
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             19               60
  1              2                2
[1] 2 2
[1] FALSE
D12V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED   11 16
  PIK3CA WILD-TYPE 29 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     11   16
  PIK3CA WILD-TYPE   29   36
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              11               29
  YES             16               36
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED               1                               41
  PIK3CA WILD-TYPE             3                              117
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  PIK3CA MUTATED                                               1
  PIK3CA WILD-TYPE                                             4
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  PIK3CA MUTATED                                     8
  PIK3CA WILD-TYPE                                  13
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  PIK3CA MUTATED                                           0
  PIK3CA WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  PIK3CA MUTATED                                              2
  PIK3CA WILD-TYPE                                            2
D12V7, multiclass
                                               clus
vv                                              PIK3CA MUTATED PIK3CA WILD-TYPE
  ADENOSQUAMOUS                                              1                3
  CERVICAL SQUAMOUS CELL CARCINOMA                          41              117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              1                4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        8               13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               2                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
D12V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  5     4
  PIK3CA WILD-TYPE                                3    15
                  vv
clus               BLACK OR AFRICAN AMERICAN
  PIK3CA MUTATED                           5
  PIK3CA WILD-TYPE                        11
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3CA MUTATED                                           1    35
  PIK3CA WILD-TYPE                                         0   103
D12V10, multiclass
                                           clus
vv                                          PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       5                3
  ASIAN                                                  4               15
  BLACK OR AFRICAN AMERICAN                              5               11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                 35              103
[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"
D12V11, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     9  30
  PIK3CA WILD-TYPE   5 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      9   30
  PIK3CA WILD-TYPE    5  105
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  9                5
  NOT HISPANIC OR LATINO             30              105
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    36  14
  PIK3CA WILD-TYPE 103  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     36   14
  PIK3CA WILD-TYPE  103   31
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  TUMOR FREE             36              103
  WITH TUMOR             14               31
[1] 2 2
[1] FALSE
                  vv
clus               G1 G2 G3 G4 GX
  PIK3CA MUTATED    6 28 17  1  1
  PIK3CA WILD-TYPE  8 60 65  0  7
D12V14, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  G1              6                8
  G2             28               60
  G3             17               65
  G4              1                0
  GX              1                7
[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"
D12V15, continuous
D12V16, continuous
D12V17, continuous
D12V18, continuous
D12V19, binary
                  cls
clus                0  1
  PIK3CA MUTATED    5  1
  PIK3CA WILD-TYPE 21  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      5    1
  PIK3CA WILD-TYPE   21    2
                         clus
vv                        PIK3CA MUTATED PIK3CA WILD-TYPE
  COMPLETED AS PLANNED                 5               21
  TREATMENT NOT COMPLETED              1                2
[1] 2 2
[1] FALSE
D12V20, continuous
D12V21, continuous
D12V22, continuous
D12V23, continuous
D12V24, continuous
D12V25, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  PIK3CA MUTATED                                     0
  PIK3CA WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  PIK3CA MUTATED                                     2                       6
  PIK3CA WILD-TYPE                                   5                      24
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  PIK3CA MUTATED                         1                       3
  PIK3CA WILD-TYPE                       0                       5
D12V26, multiclass
                                     clus
vv                                    PIK3CA MUTATED PIK3CA WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              0                1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              2                5
  OTHER LOCATION, SPECIFY                          6               24
  POSITIVE BLADDER MARGIN                          1                0
  POSITIVE VAGINAL MARGIN                          3                5
[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)
  PIK3CA MUTATED                                               0
  PIK3CA WILD-TYPE                                             3
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  PIK3CA MUTATED                                                2
  PIK3CA WILD-TYPE                                              8
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  PIK3CA MUTATED                                                                                  27
  PIK3CA WILD-TYPE                                                                                33
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  PIK3CA MUTATED                                                                                             18
  PIK3CA WILD-TYPE                                                                                           70
D12V27, multiclass
                                                                                              clus
vv                                                                                             PIK3CA MUTATED
  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)                        27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             18
                                                                                              clus
vv                                                                                             PIK3CA WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V28, binary
                  cls
clus                0  1
  PIK3CA MUTATED   17 15
  PIK3CA WILD-TYPE 46 52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     17   15
  PIK3CA WILD-TYPE   46   52
         clus
vv        PIK3CA MUTATED PIK3CA WILD-TYPE
  ABSENT              17               46
  PRESENT             15               52
[1] 2 2
[1] FALSE
D12V29, continuous
D12V30, continuous
D12V31, binary
                  cls
clus                0  1
  PIK3CA MUTATED   12 21
  PIK3CA WILD-TYPE 27 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     12   21
  PIK3CA WILD-TYPE   27   65
                                          clus
vv                                         PIK3CA MUTATED PIK3CA WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 12               27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             21               65
[1] 2 2
[1] FALSE
D12V32, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  PIK3CA MUTATED              2           9         11
  PIK3CA WILD-TYPE            6          34         35
D12V33, multiclass
              clus
vv             PIK3CA MUTATED PIK3CA WILD-TYPE
  CURRENT USER              2                6
  FORMER USER               9               34
  NEVER USED               11               35
[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"
D12V34, continuous
D12V35, binary
                  cls
clus                0  1
  PIK3CA MUTATED   21  6
  PIK3CA WILD-TYPE 67 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     21    6
  PIK3CA WILD-TYPE   67   10
         clus
vv        PIK3CA MUTATED PIK3CA WILD-TYPE
  ABSENT              21               67
  PRESENT              6               10
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  PIK3CA MUTATED             3        15     0
  PIK3CA WILD-TYPE           1        38     1
D12V36, multiclass
             clus
vv            PIK3CA MUTATED PIK3CA WILD-TYPE
  CARBOPLATIN              3                1
  CISPLATIN               15               38
  OTHER                    0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V37, continuous
D12V38, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  PIK3CA MUTATED         0        0         0         0        5        11
  PIK3CA WILD-TYPE       4        1         1         1       23        42
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  PIK3CA MUTATED          12        1         3          1          2         6
  PIK3CA WILD-TYPE        17        3         3          4          5         8
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  PIK3CA MUTATED           1          6         1         2
  PIK3CA WILD-TYPE         0         23         1         3
D12V39, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                5               23
  STAGE IB1              11               42
  STAGE IB2              12               17
  STAGE II                1                3
  STAGE IIA               3                3
  STAGE IIA1              1                4
  STAGE IIA2              2                5
  STAGE IIB               6                8
  STAGE III               1                0
  STAGE IIIB              6               23
  STAGE IVA               1                1
  STAGE IVB               2                3
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = CASP8 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     6   3
  CASP8 WILD-TYPE 144  39
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             183 
  CASP8 MUTATED CASP8 WILD-TYPE 
              3              39 
$`CASP8 MUTATED`
TCGA-C5-A1BQ TCGA-C5-A3HD TCGA-C5-A7UE TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EX-A69L 
       19.86        52.01       155.77        55.63         8.28        19.79 
TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-MY-A5BD 
       36.36       209.59        54.81 

$`CASP8 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
      147.35        17.19       131.11         9.34         1.12        95.11 
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-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
      117.99       118.65        28.90        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
       17.52        39.55        40.87        37.35        30.90        31.36 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       33.30        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01        12.13        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.43        47.77         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K 
        0.49         0.89        20.35         7.92        15.22        12.23 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 
       20.48        15.58        28.37         8.28        21.11        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.35        28.08        34.62        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  CASP8 MUTATED CASP8 WILD-TYPE 
           8.28            0.07 
  CASP8 MUTATED CASP8 WILD-TYPE 
         209.59          210.67 
  CASP8 MUTATED CASP8 WILD-TYPE 
          52.01           22.98 
[1] "8.3 - 209.6 (52.0)" "0.1 - 210.7 (23.0)"
[1] "hr=" "1.1"
D13V2, continuous
                 vv
clus               T1  T2 T3+T4
  CASP8 MUTATED     3   2     1
  CASP8 WILD-TYPE 101  38     4
D13V3, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T1                3             101
  T2                2              38
  T3+T4             1               4
[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"
D13V4, binary
                 cls
clus               0  1
  CASP8 MUTATED    5  1
  CASP8 WILD-TYPE 90 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    1
  CASP8 WILD-TYPE   90   43
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0             5              90
  1             1              43
[1] 2 2
[1] FALSE
D13V5, binary
                 cls
clus               0  1
  CASP8 MUTATED    5  0
  CASP8 WILD-TYPE 74  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    0
  CASP8 WILD-TYPE   74    4
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0             5              74
  1             0               4
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus               0  1
  CASP8 MUTATED    3  5
  CASP8 WILD-TYPE 37 47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    5
  CASP8 WILD-TYPE   37   47
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3              37
  YES             5              47
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  CASP8 MUTATED               0                                9
  CASP8 WILD-TYPE             4                              149
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  CASP8 MUTATED                                               0
  CASP8 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  CASP8 MUTATED                                     0
  CASP8 WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  CASP8 MUTATED                                           0
  CASP8 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  CASP8 MUTATED                                              0
  CASP8 WILD-TYPE                                            4
D13V7, multiclass
                                               clus
vv                                              CASP8 MUTATED CASP8 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          9             149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, continuous
D13V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                8    18
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CASP8 MUTATED                           1
  CASP8 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP8 MUTATED                                           0     7
  CASP8 WILD-TYPE                                         1   131
D13V10, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 1              18
  BLACK OR AFRICAN AMERICAN                             1              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             131
[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"
D13V11, binary
                 cls
clus                0   1
  CASP8 MUTATED     1   5
  CASP8 WILD-TYPE  13 130
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      1    5
  CASP8 WILD-TYPE   13  130
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             5             130
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                 cls
clus                0   1
  CASP8 MUTATED     8   1
  CASP8 WILD-TYPE 131  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      8    1
  CASP8 WILD-TYPE  131   44
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  TUMOR FREE             8             131
  WITH TUMOR             1              44
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  CASP8 MUTATED    1  7  1  0  0
  CASP8 WILD-TYPE 13 81 81  1  8
D13V14, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  G1             1              13
  G2             7              81
  G3             1              81
  G4             0               1
  GX             0               8
[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"
D13V15, continuous
D13V16, continuous
D13V17, continuous
D13V18, continuous
D13V19, binary
                 cls
clus               0  1
  CASP8 MUTATED    1  0
  CASP8 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      1    0
  CASP8 WILD-TYPE   25    3
                         clus
vv                        CASP8 MUTATED CASP8 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
D13V20, continuous
D13V21, continuous
D13V22, continuous
D13V23, continuous
D13V24, continuous
D13V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  CASP8 MUTATED                                     0
  CASP8 WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  CASP8 MUTATED                                     0                       1
  CASP8 WILD-TYPE                                   7                      29
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  CASP8 MUTATED                         0                       0
  CASP8 WILD-TYPE                       1                       8
D13V26, multiclass
[1] "Remove cluster labels:" "CASP8 MUTATED"         
clus
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              46 
     TCGA-EX-A449      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DR-A0ZM 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-EA-A50E      TCGA-EK-A2RC      TCGA-EK-A2RK 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EX-A1H5      TCGA-FU-A3EO      TCGA-HM-A4S6 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-MU-A51Y 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  CASP8 MUTATED                                               0
  CASP8 WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  CASP8 MUTATED                                                0
  CASP8 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  CASP8 MUTATED                                                                                   4
  CASP8 WILD-TYPE                                                                                56
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  CASP8 MUTATED                                                                                              3
  CASP8 WILD-TYPE                                                                                           85
D13V27, multiclass
                                                                                              clus
vv                                                                                             CASP8 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             3
                                                                                              clus
vv                                                                                             CASP8 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V28, binary
                 cls
clus               0  1
  CASP8 MUTATED    0  4
  CASP8 WILD-TYPE 63 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0    4
  CASP8 WILD-TYPE   63   63
         clus
vv        CASP8 MUTATED CASP8 WILD-TYPE
  ABSENT              0              63
  PRESENT             4              63
[1] 2 2
[1] FALSE
D13V29, continuous
D13V30, continuous
D13V31, binary
                 cls
clus               0  1
  CASP8 MUTATED    2  3
  CASP8 WILD-TYPE 37 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      2    3
  CASP8 WILD-TYPE   37   83
                                          clus
vv                                         CASP8 MUTATED CASP8 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 2              37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             3              83
[1] 2 2
[1] FALSE
D13V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  CASP8 MUTATED              0           1          4
  CASP8 WILD-TYPE            8          42         42
D13V33, multiclass
              clus
vv             CASP8 MUTATED CASP8 WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              1              42
  NEVER USED               4              42
[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"
D13V34, continuous
D13V35, binary
                 cls
clus               0  1
  CASP8 MUTATED    2  1
  CASP8 WILD-TYPE 86 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      2    1
  CASP8 WILD-TYPE   86   15
         clus
vv        CASP8 MUTATED CASP8 WILD-TYPE
  ABSENT              2              86
  PRESENT             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  CASP8 MUTATED             0         4     0
  CASP8 WILD-TYPE           4        49     1
D13V36, multiclass
             clus
vv            CASP8 MUTATED CASP8 WILD-TYPE
  CARBOPLATIN             0               4
  CISPLATIN               4              49
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V37, continuous
D13V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  CASP8 MUTATED         0        0         0         0        1         3
  CASP8 WILD-TYPE       4        1         1         1       27        50
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  CASP8 MUTATED           0        0         0          0          1         2
  CASP8 WILD-TYPE        29        4         6          5          6        12
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  CASP8 MUTATED           1          1         0         0
  CASP8 WILD-TYPE         0         28         2         5
D13V39, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              3              50
  STAGE IB2              0              29
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             1               6
  STAGE IIB              2              12
  STAGE III              1               0
  STAGE IIIB             1              28
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = FAT2 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  FAT2 MUTATED     9   2
  FAT2 WILD-TYPE 141  40
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            181 
  FAT2 MUTATED FAT2 WILD-TYPE 
             2             40 
$`FAT2 MUTATED`
TCGA-C5-A1MN TCGA-C5-A7UE TCGA-DR-A0ZM TCGA-EA-A6QX TCGA-EK-A2PG TCGA-FU-A3TQ 
       40.93       155.77        58.88        24.00         1.51        26.14 
TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL TCGA-Q1-A73O 
      137.16        78.71        29.85        15.58        14.07 

$`FAT2 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH 
       20.35       147.35        17.19       131.11         9.34         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       95.11        82.06        44.94        63.98        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
       55.63       117.99       118.65        28.90        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
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-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       27.22        13.48        60.72        26.27         6.64        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.89         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       40.96         0.30         4.24         0.07         1.87         1.74 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.43        47.77         1.64         2.33         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.49         0.89        20.35         7.92        15.22        19.79 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       12.23        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       20.98        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL 
      147.39        66.81       129.37        96.95        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        20.48        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89        12.49         0.30         0.82        13.35        28.08 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       34.62        54.81        35.05        20.84        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95         9.04        16.14        17.56        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-WL-A834 
       26.01 

  FAT2 MUTATED FAT2 WILD-TYPE 
          1.51           0.07 
  FAT2 MUTATED FAT2 WILD-TYPE 
        155.77         210.67 
  FAT2 MUTATED FAT2 WILD-TYPE 
         29.85          22.62 
[1] "1.5 - 155.8 (29.9)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1.8"
D14V2, continuous
                vv
clus              T1  T2 T3+T4
  FAT2 MUTATED     4   3     0
  FAT2 WILD-TYPE 100  37     5
D14V3, multiclass
       clus
vv      FAT2 MUTATED FAT2 WILD-TYPE
  T1               4            100
  T2               3             37
  T3+T4            0              5
[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"
D14V4, binary
                cls
clus              0  1
  FAT2 MUTATED    4  2
  FAT2 WILD-TYPE 91 42
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      4    2
  FAT2 WILD-TYPE   91   42
   clus
vv  FAT2 MUTATED FAT2 WILD-TYPE
  0            4             91
  1            2             42
[1] 2 2
[1] FALSE
D14V5, binary
                cls
clus              0  1
  FAT2 MUTATED    5  0
  FAT2 WILD-TYPE 74  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      5    0
  FAT2 WILD-TYPE   74    4
   clus
vv  FAT2 MUTATED FAT2 WILD-TYPE
  0            5             74
  1            0              4
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus              0  1
  FAT2 MUTATED    1  4
  FAT2 WILD-TYPE 39 48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      1    4
  FAT2 WILD-TYPE   39   48
     clus
vv    FAT2 MUTATED FAT2 WILD-TYPE
  NO             1             39
  YES            4             48
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  FAT2 MUTATED               0                               10
  FAT2 WILD-TYPE             4                              148
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  FAT2 MUTATED                                               0
  FAT2 WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  FAT2 MUTATED                                     0
  FAT2 WILD-TYPE                                  21
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  FAT2 MUTATED                                           1
  FAT2 WILD-TYPE                                         1
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  FAT2 MUTATED                                              0
  FAT2 WILD-TYPE                                            4
D14V7, multiclass
                                               clus
vv                                              FAT2 MUTATED FAT2 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                        10            148
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, continuous
D14V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT2 MUTATED                                  1     1
  FAT2 WILD-TYPE                                7    18
                vv
clus             BLACK OR AFRICAN AMERICAN
  FAT2 MUTATED                           2
  FAT2 WILD-TYPE                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAT2 MUTATED                                           0     6
  FAT2 WILD-TYPE                                         1   132
D14V10, multiclass
                                           clus
vv                                          FAT2 MUTATED FAT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              7
  ASIAN                                                1             18
  BLACK OR AFRICAN AMERICAN                            2             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            132
[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"
D14V11, binary
                cls
clus               0   1
  FAT2 MUTATED     2   4
  FAT2 WILD-TYPE  12 131
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      2    4
  FAT2 WILD-TYPE   12  131
                        clus
vv                       FAT2 MUTATED FAT2 WILD-TYPE
  HISPANIC OR LATINO                2             12
  NOT HISPANIC OR LATINO            4            131
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                cls
clus               0   1
  FAT2 MUTATED     9   1
  FAT2 WILD-TYPE 130  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      9    1
  FAT2 WILD-TYPE  130   44
            clus
vv           FAT2 MUTATED FAT2 WILD-TYPE
  TUMOR FREE            9            130
  WITH TUMOR            1             44
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  FAT2 MUTATED    1  4  4  1  1
  FAT2 WILD-TYPE 13 84 78  0  7
D14V14, multiclass
    clus
vv   FAT2 MUTATED FAT2 WILD-TYPE
  G1            1             13
  G2            4             84
  G3            4             78
  G4            1              0
  GX            1              7
[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"
D14V15, continuous
[1] "Remove cluster labels:" "FAT2 MUTATED"          
clus
  FAT2 MUTATED FAT2 WILD-TYPE 
             1             28 
    TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-C5-A1BJ 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BQ     TCGA-C5-A1ME     TCGA-C5-A1MF 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A7CM 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DS-A3LQ     TCGA-EK-A2RA 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-FU-A2QG     TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LB     TCGA-JX-A3Q0     TCGA-MU-A5YI 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
D14V16, continuous
D14V17, continuous
D14V18, continuous
D14V19, binary
                cls
clus              0  1
  FAT2 MUTATED    2  0
  FAT2 WILD-TYPE 24  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      2    0
  FAT2 WILD-TYPE   24    3
                         clus
vv                        FAT2 MUTATED FAT2 WILD-TYPE
  COMPLETED AS PLANNED               2             24
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D14V20, continuous
D14V21, continuous
D14V22, continuous
D14V23, continuous
D14V24, continuous
D14V25, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FAT2 MUTATED                                     0
  FAT2 WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FAT2 MUTATED                                     1                       1
  FAT2 WILD-TYPE                                   6                      29
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FAT2 MUTATED                         0                       1
  FAT2 WILD-TYPE                       1                       7
D14V26, multiclass
                                     clus
vv                                    FAT2 MUTATED FAT2 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            1              6
  OTHER LOCATION, SPECIFY                        1             29
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              7
[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)
  FAT2 MUTATED                                               0
  FAT2 WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  FAT2 MUTATED                                                1
  FAT2 WILD-TYPE                                              9
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  FAT2 MUTATED                                                                                   5
  FAT2 WILD-TYPE                                                                                55
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  FAT2 MUTATED                                                                                              4
  FAT2 WILD-TYPE                                                                                           84
D14V27, multiclass
                                                                                              clus
vv                                                                                             FAT2 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                          1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                       5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            4
                                                                                              clus
vv                                                                                             FAT2 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V28, binary
                cls
clus              0  1
  FAT2 MUTATED    2  4
  FAT2 WILD-TYPE 61 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      2    4
  FAT2 WILD-TYPE   61   63
         clus
vv        FAT2 MUTATED FAT2 WILD-TYPE
  ABSENT             2             61
  PRESENT            4             63
[1] 2 2
[1] FALSE
D14V29, continuous
D14V30, continuous
D14V31, binary
                cls
clus              0  1
  FAT2 MUTATED    1  5
  FAT2 WILD-TYPE 38 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      1    5
  FAT2 WILD-TYPE   38   81
                                          clus
vv                                         FAT2 MUTATED FAT2 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                1             38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            5             81
[1] 2 2
[1] FALSE
D14V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  FAT2 MUTATED              0           3          2
  FAT2 WILD-TYPE            8          40         44
D14V33, multiclass
              clus
vv             FAT2 MUTATED FAT2 WILD-TYPE
  CURRENT USER            0              8
  FORMER USER             3             40
  NEVER USED              2             44
[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"
D14V34, continuous
D14V35, binary
                cls
clus              0  1
  FAT2 MUTATED    5  2
  FAT2 WILD-TYPE 83 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      5    2
  FAT2 WILD-TYPE   83   14
         clus
vv        FAT2 MUTATED FAT2 WILD-TYPE
  ABSENT             5             83
  PRESENT            2             14
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  FAT2 MUTATED             0         6     0
  FAT2 WILD-TYPE           4        47     1
D14V36, multiclass
             clus
vv            FAT2 MUTATED FAT2 WILD-TYPE
  CARBOPLATIN            0              4
  CISPLATIN              6             47
  OTHER                  0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V37, continuous
[1] "Remove cluster labels:" "FAT2 MUTATED"          
clus
  FAT2 MUTATED FAT2 WILD-TYPE 
             1              9 
    TCGA-C5-A1BN     TCGA-C5-A1MH     TCGA-C5-A1ML     TCGA-C5-A1MP 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-HM-A3JK     TCGA-JW-A852     TCGA-JX-A3Q8 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-MU-A51Y 
"FAT2 WILD-TYPE" 
D14V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  FAT2 MUTATED         0        0         0         0        0         2
  FAT2 WILD-TYPE       4        1         1         1       28        51
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  FAT2 MUTATED           3        0         0          1          0         0
  FAT2 WILD-TYPE        26        4         6          4          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  FAT2 MUTATED           0          4         0         0
  FAT2 WILD-TYPE         1         25         2         5
D14V39, multiclass
            clus
vv           FAT2 MUTATED FAT2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              0             28
  STAGE IB1             2             51
  STAGE IB2             3             26
  STAGE II              0              4
  STAGE IIA             0              6
  STAGE IIA1            1              4
  STAGE IIA2            0              7
  STAGE IIB             0             14
  STAGE III             0              1
  STAGE IIIB            4             25
  STAGE IVA             0              2
  STAGE IVB             0              5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = ZNF750 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED     7   1
  ZNF750 WILD-TYPE 143  41
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               8              184 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               1               41 
$`ZNF750 MUTATED`
TCGA-C5-A1BQ TCGA-C5-A3HE TCGA-DR-A0ZM TCGA-FU-A3TQ TCGA-JW-A5VL TCGA-LP-A5U2 
       19.86        18.02        58.88        26.14        15.58         0.30 
TCGA-LP-A5U3 TCGA-Q1-A73O 
        0.82        14.07 

$`ZNF750 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        52.01        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH 
      147.35        17.19       155.77       131.11         9.34         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       95.11        82.06        44.94        63.98        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
       55.63       117.99       118.65        28.90        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
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-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        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-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        1.51        19.27         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        1.87         1.74         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       15.22        19.79        12.23        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       31.36        36.26        20.98        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       35.44        10.55         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        20.48        28.37         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
       12.49        13.35        28.08        34.62        54.81        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       20.84        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       14.60        11.67        93.99        26.01 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
            0.30             0.07 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           58.88           210.67 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           16.80            24.28 
[1] "0.3 - 58.9 (16.8)"  "0.1 - 210.7 (24.3)"
[1] "hr=" "1.1"
D15V2, continuous
                  vv
clus                T1  T2 T3+T4
  ZNF750 MUTATED     4   3     0
  ZNF750 WILD-TYPE 100  37     5
D15V3, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T1                 4              100
  T2                 3               37
  T3+T4              0                5
[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"
D15V4, binary
                  cls
clus                0  1
  ZNF750 MUTATED    4  2
  ZNF750 WILD-TYPE 91 42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      4    2
  ZNF750 WILD-TYPE   91   42
   clus
vv  ZNF750 MUTATED ZNF750 WILD-TYPE
  0              4               91
  1              2               42
[1] 2 2
[1] FALSE
D15V5, binary
                  cls
clus                0  1
  ZNF750 MUTATED    4  0
  ZNF750 WILD-TYPE 75  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      4    0
  ZNF750 WILD-TYPE   75    4
   clus
vv  ZNF750 MUTATED ZNF750 WILD-TYPE
  0              4               75
  1              0                4
[1] 2 2
[1] FALSE
D15V6, binary
                  cls
clus                0  1
  ZNF750 MUTATED    3  3
  ZNF750 WILD-TYPE 37 49
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3    3
  ZNF750 WILD-TYPE   37   49
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               3               37
  YES              3               49
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ZNF750 MUTATED               0                                8
  ZNF750 WILD-TYPE             4                              150
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  ZNF750 MUTATED                                               1
  ZNF750 WILD-TYPE                                             4
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  ZNF750 MUTATED                                     0
  ZNF750 WILD-TYPE                                  21
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  ZNF750 MUTATED                                           0
  ZNF750 WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  ZNF750 MUTATED                                              0
  ZNF750 WILD-TYPE                                            4
D15V7, multiclass
                                               clus
vv                                              ZNF750 MUTATED ZNF750 WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           8              150
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              1                4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        0               21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, continuous
D15V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF750 MUTATED                                  1     3
  ZNF750 WILD-TYPE                                7    16
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF750 MUTATED                           0
  ZNF750 WILD-TYPE                        16
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF750 MUTATED                                           0     4
  ZNF750 WILD-TYPE                                         1   134
D15V10, multiclass
                                           clus
vv                                          ZNF750 MUTATED ZNF750 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                7
  ASIAN                                                  3               16
  BLACK OR AFRICAN AMERICAN                              0               16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              134
[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"
D15V11, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     2   7
  ZNF750 WILD-TYPE  12 128
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    7
  ZNF750 WILD-TYPE   12  128
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  2               12
  NOT HISPANIC OR LATINO              7              128
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     8   0
  ZNF750 WILD-TYPE 131  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      8    0
  ZNF750 WILD-TYPE  131   45
            clus
vv           ZNF750 MUTATED ZNF750 WILD-TYPE
  TUMOR FREE              8              131
  WITH TUMOR              0               45
[1] 2 2
[1] FALSE
                  vv
clus               G1 G2 G3 G4 GX
  ZNF750 MUTATED    1  4  3  0  1
  ZNF750 WILD-TYPE 13 84 79  1  7
D15V14, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  G1              1               13
  G2              4               84
  G3              3               79
  G4              0                1
  GX              1                7
[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"
D15V15, continuous
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               1               28 
      TCGA-EX-A69M       TCGA-FU-A3TX       TCGA-BI-A0VR       TCGA-C5-A1BJ 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1BL       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A2M2       TCGA-C5-A3HD       TCGA-C5-A7CM       TCGA-C5-A7CO 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DG-A2KK       TCGA-DS-A3LQ       TCGA-EK-A2RA       TCGA-FU-A2QG 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-IR-A3L7 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-JX-A3Q0       TCGA-MU-A5YI 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
D15V16, continuous
D15V17, continuous
D15V18, continuous
D15V19, binary
                  cls
clus                0  1
  ZNF750 MUTATED    1  0
  ZNF750 WILD-TYPE 25  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      1    0
  ZNF750 WILD-TYPE   25    3
                         clus
vv                        ZNF750 MUTATED ZNF750 WILD-TYPE
  COMPLETED AS PLANNED                 1               25
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
D15V20, continuous
D15V21, continuous
D15V22, continuous
D15V23, continuous
D15V24, continuous
D15V25, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ZNF750 MUTATED                                     0
  ZNF750 WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ZNF750 MUTATED                                     0                       2
  ZNF750 WILD-TYPE                                   7                      28
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ZNF750 MUTATED                         0                       0
  ZNF750 WILD-TYPE                       1                       8
D15V26, multiclass
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               45 
      TCGA-EX-A449       TCGA-BI-A20A       TCGA-C5-A0TN       TCGA-C5-A1BE 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1MJ       TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2M1 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7CJ       TCGA-C5-A7UC 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DS-A0VK       TCGA-DS-A0VL 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EA-A50E       TCGA-EK-A2RC       TCGA-EK-A2RK       TCGA-EK-A2RN 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A3EO       TCGA-HM-A4S6       TCGA-IR-A3LH 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LI       TCGA-IR-A3LK       TCGA-MU-A51Y       TCGA-UC-A7PD 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-WL-A834 
"ZNF750 WILD-TYPE" 
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ZNF750 MUTATED                                               0
  ZNF750 WILD-TYPE                                             3
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  ZNF750 MUTATED                                                0
  ZNF750 WILD-TYPE                                             10
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  ZNF750 MUTATED                                                                                   3
  ZNF750 WILD-TYPE                                                                                57
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ZNF750 MUTATED                                                                                              4
  ZNF750 WILD-TYPE                                                                                           84
D15V27, multiclass
                                                                                              clus
vv                                                                                             ZNF750 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              4
                                                                                              clus
vv                                                                                             ZNF750 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V28, binary
                  cls
clus                0  1
  ZNF750 MUTATED    2  3
  ZNF750 WILD-TYPE 61 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    3
  ZNF750 WILD-TYPE   61   64
         clus
vv        ZNF750 MUTATED ZNF750 WILD-TYPE
  ABSENT               2               61
  PRESENT              3               64
[1] 2 2
[1] FALSE
D15V29, continuous
D15V30, continuous
D15V31, binary
                  cls
clus                0  1
  ZNF750 MUTATED    1  6
  ZNF750 WILD-TYPE 38 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      1    6
  ZNF750 WILD-TYPE   38   80
                                          clus
vv                                         ZNF750 MUTATED ZNF750 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  1               38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              6               80
[1] 2 2
[1] FALSE
D15V32, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  ZNF750 MUTATED              0           1          2
  ZNF750 WILD-TYPE            8          42         44
D15V33, multiclass
              clus
vv             ZNF750 MUTATED ZNF750 WILD-TYPE
  CURRENT USER              0                8
  FORMER USER               1               42
  NEVER USED                2               44
[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"
D15V34, continuous
D15V35, binary
                  cls
clus                0  1
  ZNF750 MUTATED    3  2
  ZNF750 WILD-TYPE 85 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3    2
  ZNF750 WILD-TYPE   85   14
         clus
vv        ZNF750 MUTATED ZNF750 WILD-TYPE
  ABSENT               3               85
  PRESENT              2               14
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  ZNF750 MUTATED             0         4     0
  ZNF750 WILD-TYPE           4        49     1
D15V36, multiclass
             clus
vv            ZNF750 MUTATED ZNF750 WILD-TYPE
  CARBOPLATIN              0                4
  CISPLATIN                4               49
  OTHER                    0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V37, continuous
D15V38, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  ZNF750 MUTATED         0        0         0         0        1         1
  ZNF750 WILD-TYPE       4        1         1         1       27        52
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  ZNF750 MUTATED           3        0         0          0          0         0
  ZNF750 WILD-TYPE        26        4         6          5          7        14
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  ZNF750 MUTATED           0          4         0         0
  ZNF750 WILD-TYPE         1         25         2         5
D15V39, multiclass
            clus
vv           ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                1               27
  STAGE IB1               1               52
  STAGE IB2               3               26
  STAGE II                0                4
  STAGE IIA               0                6
  STAGE IIA1              0                5
  STAGE IIA2              0                7
  STAGE IIB               0               14
  STAGE III               0                1
  STAGE IIIB              4               25
  STAGE IVA               0                2
  STAGE IVB               0                5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = C12ORF43 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     4   0
  C12ORF43 WILD-TYPE 146  42
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                188 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 0                 42 
$`C12ORF43 MUTATED`
TCGA-BI-A20A TCGA-DR-A0ZM TCGA-EK-A2H0 TCGA-JX-A3Q0 
       23.67        58.88        60.72       209.59 

$`C12ORF43 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       11.44        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76        55.63       117.99       118.65        28.90        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.36        33.30        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.25        27.22        24.00        13.48        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        1.51        19.27         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        1.87         1.74         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       15.22        19.79        12.23        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
       14.01        35.44        10.55         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       28.37         8.28        21.11        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89        12.49         0.30         0.82        13.35        28.08 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       34.62        54.81        35.05        20.84        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             23.67               0.07 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
            209.59             210.67 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
              59.8               22.8 
[1] "23.7 - 209.6 (59.8)" "0.1 - 210.7 (22.8)" 
[1] "hr="     "2.6e+07"
D16V2, continuous
                    vv
clus                  T1  T2 T3+T4
  C12ORF43 MUTATED     1   1     1
  C12ORF43 WILD-TYPE 103  39     4
D16V3, multiclass
       clus
vv      C12ORF43 MUTATED C12ORF43 WILD-TYPE
  T1                   1                103
  T2                   1                 39
  T3+T4                1                  4
[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"
D16V4, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    3  0
  C12ORF43 WILD-TYPE 92 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      3    0
  C12ORF43 WILD-TYPE   92   44
   clus
vv  C12ORF43 MUTATED C12ORF43 WILD-TYPE
  0                3                 92
  1                0                 44
[1] 2 2
[1] FALSE
D16V5, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    3  0
  C12ORF43 WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      3    0
  C12ORF43 WILD-TYPE   76    4
   clus
vv  C12ORF43 MUTATED C12ORF43 WILD-TYPE
  0                3                 76
  1                0                  4
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    1  2
  C12ORF43 WILD-TYPE 39 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    2
  C12ORF43 WILD-TYPE   39   50
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 1                 39
  YES                2                 50
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  C12ORF43 MUTATED               0                                4
  C12ORF43 WILD-TYPE             4                              154
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  C12ORF43 MUTATED                                               0
  C12ORF43 WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  C12ORF43 MUTATED                                     0
  C12ORF43 WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  C12ORF43 MUTATED                                           0
  C12ORF43 WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  C12ORF43 MUTATED                                              0
  C12ORF43 WILD-TYPE                                            4
D16V7, multiclass
                                               clus
vv                                              C12ORF43 MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             4
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              C12ORF43 WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 55 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M2         TCGA-C5-A3HD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-EA-A556         TCGA-EX-A1H5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-WL-A834 
"C12ORF43 WILD-TYPE" 
D16V9, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                119 
        TCGA-EX-A69M         TCGA-FU-A3TX         TCGA-BI-A0VR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BK         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1M5         TCGA-C5-A1M7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2M1         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7UE         TCGA-DG-A2KH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KJ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KM         TCGA-DR-A0ZL         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A43B         TCGA-EA-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A50E         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5FO         TCGA-EA-A5O9         TCGA-EA-A6QX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-EK-A2RO         TCGA-EK-A3GK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A23K         TCGA-FU-A23L 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A40J 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A57G         TCGA-FU-A5XV         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JX-A3PZ         TCGA-JX-A3Q8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-LP-A4AX         TCGA-LP-A5U2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A7HU         TCGA-MU-A51Y         TCGA-MU-A5YI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MY-A5BD         TCGA-MY-A5BF         TCGA-Q1-A5R1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-R2-A69V         TCGA-RA-A741         TCGA-UC-A7PD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PF         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF43 MUTATED                                  0     0
  C12ORF43 WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  C12ORF43 MUTATED                           1
  C12ORF43 WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C12ORF43 MUTATED                                           0     3
  C12ORF43 WILD-TYPE                                         1   135
D16V10, multiclass
                                           clus
vv                                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                1                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                135
[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"
D16V11, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   3
  C12ORF43 WILD-TYPE  14 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    3
  C12ORF43 WILD-TYPE   14  132
                        clus
vv                       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO                3                132
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     4   0
  C12ORF43 WILD-TYPE 135  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      4    0
  C12ORF43 WILD-TYPE  135   45
            clus
vv           C12ORF43 MUTATED C12ORF43 WILD-TYPE
  TUMOR FREE                4                135
  WITH TUMOR                0                 45
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  C12ORF43 MUTATED    0  2  2  0  0
  C12ORF43 WILD-TYPE 14 86 80  1  8
D16V14, multiclass
    clus
vv   C12ORF43 MUTATED C12ORF43 WILD-TYPE
  G1                0                 14
  G2                2                 86
  G3                2                 80
  G4                0                  1
  GX                0                  8
[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"
D16V15, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                 28 
        TCGA-EX-A69M         TCGA-FU-A3TX         TCGA-BI-A0VR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-DG-A2KK         TCGA-DS-A3LQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-FU-A2QG         TCGA-FU-A3WB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-MU-A5YI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-WL-A834 
"C12ORF43 WILD-TYPE" 
D16V16, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 55 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M2         TCGA-C5-A3HD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-EA-A556         TCGA-EX-A1H5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-WL-A834 
"C12ORF43 WILD-TYPE" 
D16V17, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                163 
        TCGA-EX-A69M         TCGA-FU-A3TX         TCGA-BI-A0VR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CM         TCGA-C5-A7CO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KH         TCGA-DG-A2KK         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KM         TCGA-DR-A0ZL         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A439 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EA-A44S         TCGA-EA-A4BA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EA-A556         TCGA-EA-A5FO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A5ZD         TCGA-EA-A5ZE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZF         TCGA-EA-A6QX         TCGA-EA-A78R 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-EK-A2RB         TCGA-EK-A3GM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A23K         TCGA-FU-A23L 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A40J 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A57G         TCGA-FU-A5XV         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JW-A5VG         TCGA-JW-A5VH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AU         TCGA-LP-A4AV         TCGA-LP-A4AW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AX         TCGA-LP-A5U2         TCGA-LP-A5U3 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A7HU         TCGA-MU-A51Y         TCGA-MU-A5YI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MY-A5BD         TCGA-MY-A5BE         TCGA-MY-A5BF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A5R2         TCGA-Q1-A5R3 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A6DT         TCGA-Q1-A6DV         TCGA-Q1-A6DW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73O         TCGA-Q1-A73P         TCGA-Q1-A73Q 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73R         TCGA-Q1-A73S         TCGA-R2-A69V 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-WL-A834 
"C12ORF43 WILD-TYPE" 
D16V18, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 50 
        TCGA-FU-A3TX         TCGA-BI-A0VR         TCGA-C5-A1BI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M2         TCGA-C5-A3HD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-EA-A556         TCGA-EK-A2RA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-Q1-A6DW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V19, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    1  1
  C12ORF43 WILD-TYPE 25  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    1
  C12ORF43 WILD-TYPE   25    2
                         clus
vv                        C12ORF43 MUTATED C12ORF43 WILD-TYPE
  COMPLETED AS PLANNED                   1                 25
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D16V20, continuous
D16V21, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                100 
        TCGA-EX-A449         TCGA-BI-A0VR         TCGA-BI-A0VS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-FU-A2QG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A770         TCGA-HG-A2PA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-IR-A3L7         TCGA-IR-A3LC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VH         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A5VL         TCGA-JW-A69B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3PZ         TCGA-JX-A3Q8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-RA-A741         TCGA-UC-A7PD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PF 
"C12ORF43 WILD-TYPE" 
D16V22, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                108 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HU         TCGA-EA-A3QD         TCGA-EA-A3QE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A556         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZD         TCGA-EK-A2IP         TCGA-EK-A2RK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A57G         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JW-A5VG         TCGA-JW-A5VH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V23, continuous
D16V24, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                108 
        TCGA-EX-A449         TCGA-BI-A0VS         TCGA-C5-A0TN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HU         TCGA-EA-A3QD         TCGA-EA-A3QE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A6QX         TCGA-EK-A2RN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H6         TCGA-FU-A2QG         TCGA-FU-A3EO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A770         TCGA-HG-A2PA         TCGA-HM-A3JJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-IR-A3L7         TCGA-IR-A3LC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VH         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A5VL         TCGA-JW-A69B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3PZ         TCGA-JX-A3Q8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-LP-A5U2         TCGA-MU-A51Y 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V25, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                102 
        TCGA-EX-A69M         TCGA-BI-A0VR         TCGA-BI-A0VS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-FU-A2QG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A5XV         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-IR-A3L7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-JX-A5QV         TCGA-Q1-A73Q 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  C12ORF43 MUTATED                                     0
  C12ORF43 WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  C12ORF43 MUTATED                                     1
  C12ORF43 WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  C12ORF43 MUTATED                         1                       0
  C12ORF43 WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  C12ORF43 MUTATED                         0
  C12ORF43 WILD-TYPE                       8
D16V26, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 45 
        TCGA-EX-A449         TCGA-C5-A0TN         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BM         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A3HE         TCGA-C5-A3HL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CJ         TCGA-C5-A7UC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-EA-A50E 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RC         TCGA-EK-A2RK         TCGA-EK-A2RN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A3EO         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-UC-A7PD         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  C12ORF43 MUTATED                                               0
  C12ORF43 WILD-TYPE                                             3
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  C12ORF43 MUTATED                                                0
  C12ORF43 WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  C12ORF43 MUTATED                                                                                   2
  C12ORF43 WILD-TYPE                                                                                58
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  C12ORF43 MUTATED                                                                                              1
  C12ORF43 WILD-TYPE                                                                                           87
D16V27, multiclass
                                                                                              clus
vv                                                                                             C12ORF43 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                1
                                                                                              clus
vv                                                                                             C12ORF43 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V28, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    0  2
  C12ORF43 WILD-TYPE 63 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    2
  C12ORF43 WILD-TYPE   63   65
         clus
vv        C12ORF43 MUTATED C12ORF43 WILD-TYPE
  ABSENT                 0                 63
  PRESENT                2                 65
[1] 2 2
[1] FALSE
D16V29, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                119 
        TCGA-EX-A69M         TCGA-FU-A3TX         TCGA-BI-A0VR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BK         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1M5         TCGA-C5-A1M7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2M1         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7UE         TCGA-DG-A2KH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KJ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KM         TCGA-DR-A0ZL         TCGA-DS-A0VK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A43B         TCGA-EA-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A50E         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5FO         TCGA-EA-A5O9         TCGA-EA-A6QX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-EK-A2RO         TCGA-EK-A3GK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A23K         TCGA-FU-A23L 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A40J 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A57G         TCGA-FU-A5XV         TCGA-FU-A770 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JX-A3PZ         TCGA-JX-A3Q8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-LP-A4AX         TCGA-LP-A5U2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A7HU         TCGA-MU-A51Y         TCGA-MU-A5YI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MY-A5BD         TCGA-MY-A5BF         TCGA-Q1-A5R1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-R2-A69V         TCGA-RA-A741         TCGA-UC-A7PD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PF         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V30, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                138 
        TCGA-EK-A2GZ         TCGA-EX-A69M         TCGA-FU-A3TX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A0TN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BF         TCGA-C5-A1BK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1M5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MP         TCGA-C5-A1MQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7UC         TCGA-C5-A7UE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KH         TCGA-DG-A2KJ         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KL         TCGA-DG-A2KM         TCGA-DR-A0ZL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A1OA         TCGA-DS-A3LQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HU         TCGA-EA-A3QD         TCGA-EA-A3QE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EA-A44S         TCGA-EA-A4BA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EA-A556         TCGA-EA-A5FO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A6QX         TCGA-EK-A2IP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2PK         TCGA-EK-A2R7         TCGA-EK-A2R8 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2R9         TCGA-EK-A2RA         TCGA-EK-A2RC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RD         TCGA-EK-A2RE         TCGA-EK-A2RJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RK         TCGA-EK-A2RL         TCGA-EK-A2RM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RN         TCGA-EK-A2RO         TCGA-EK-A3GJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A3GK         TCGA-EX-A1H5         TCGA-EX-A1H6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-EX-A69L         TCGA-FU-A23K 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A40J         TCGA-FU-A57G         TCGA-FU-A5XV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A770         TCGA-HG-A2PA         TCGA-HM-A3JJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-HM-A6W2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LA         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AV         TCGA-LP-A4AW         TCGA-LP-A4AX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-LP-A7HU         TCGA-MU-A51Y 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MY-A5BD         TCGA-MY-A5BF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A6DV         TCGA-Q1-A73P 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-R2-A69V         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V31, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    1  3
  C12ORF43 WILD-TYPE 38 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    3
  C12ORF43 WILD-TYPE   38   83
                                          clus
vv                                         C12ORF43 MUTATED C12ORF43 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                3                 83
[1] 2 2
[1] FALSE
D16V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  C12ORF43 MUTATED              0           1          1
  C12ORF43 WILD-TYPE            8          42         45
D16V33, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 95 
        TCGA-EX-A69M         TCGA-C5-A1BI         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M6         TCGA-C5-A1M7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MN         TCGA-C5-A2LT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7UH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DG-A2KM         TCGA-DR-A0ZL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A1OA         TCGA-DS-A3LQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HT         TCGA-EA-A3HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A43B         TCGA-EA-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A50E         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A5ZE         TCGA-EA-A5ZF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2R7         TCGA-EK-A3GK         TCGA-EX-A1H5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H6         TCGA-EX-A3L1         TCGA-EX-A69L 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A57G 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LA         TCGA-IR-A3LB         TCGA-IR-A3LC 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-JW-A5VG         TCGA-JW-A5VI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A69B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-LP-A5U3         TCGA-LP-A7HU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A5R2         TCGA-Q1-A5R3 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V34, continuous
D16V35, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    0  2
  C12ORF43 WILD-TYPE 88 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    2
  C12ORF43 WILD-TYPE   88   14
         clus
vv        C12ORF43 MUTATED C12ORF43 WILD-TYPE
  ABSENT                 0                 88
  PRESENT                2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  C12ORF43 MUTATED             0         2     0
  C12ORF43 WILD-TYPE           4        51     1
D16V36, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 56 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M9         TCGA-C5-A1MH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LT         TCGA-C5-A2LX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A3HD         TCGA-C5-A7CJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CM 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DG-A2KJ         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DG-A2KM         TCGA-DS-A0VM         TCGA-DS-A0VN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EK-A2H1         TCGA-HM-A3JJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3LA         TCGA-IR-A3LB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-LP-A4AU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R2         TCGA-Q1-A5R3         TCGA-Q1-A6DW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73O         TCGA-Q1-A73Q         TCGA-Q1-A73S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-R2-A69V         TCGA-RA-A741 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D16V37, continuous
D16V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  C12ORF43 MUTATED         0        0         0         0        0         1
  C12ORF43 WILD-TYPE       4        1         1         1       28        52
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  C12ORF43 MUTATED           0        0         0          0          0
  C12ORF43 WILD-TYPE        29        4         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  C12ORF43 MUTATED           1         1          1         0         0
  C12ORF43 WILD-TYPE        13         0         28         2         5
D16V39, multiclass
            clus
vv           C12ORF43 MUTATED C12ORF43 WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 28
  STAGE IB1                 1                 52
  STAGE IB2                 0                 29
  STAGE II                  0                  4
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 1                 13
  STAGE III                 1                  0
  STAGE IIIB                1                 28
  STAGE IVA                 0                  2
  STAGE IVB                 0                  5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = C3ORF70 MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  C3ORF70 MUTATED     4   0
  C3ORF70 WILD-TYPE 146  42
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                4               188 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                0                42 
$`C3ORF70 MUTATED`
TCGA-EA-A439 TCGA-EK-A3GK TCGA-MY-A5BD TCGA-Q1-A6DW 
       31.73         0.49        54.81        17.56 

$`C3ORF70 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        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-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        3.58        33.90        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        9.34         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63       117.99       118.65 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       28.90        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU 
       39.55        40.87        37.35        30.90        31.36        33.30 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05        25.02        36.89        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.13        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       27.29        27.25        27.22        24.00        13.48        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.89         1.45         0.13        40.96         0.30 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL 
        4.24         0.07         1.87         1.74         0.43        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        1.64         2.33         0.07         0.10         0.89        20.35 
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-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       28.31        14.01        35.44        10.55         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58        28.37         8.28        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.35        28.08        34.62        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95         9.04        16.14        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
             0.49              0.07 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
            54.81            210.67 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
           24.645            23.755 
[1] "0.5 - 54.8 (24.6)"  "0.1 - 210.7 (23.8)"
[1] "hr="     "9200000"
D17V2, continuous
                   vv
clus                 T1  T2 T3+T4
  C3ORF70 MUTATED     1   2     0
  C3ORF70 WILD-TYPE 103  38     5
D17V3, multiclass
       clus
vv      C3ORF70 MUTATED C3ORF70 WILD-TYPE
  T1                  1               103
  T2                  2                38
  T3+T4               0                 5
[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"
D17V4, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    3  0
  C3ORF70 WILD-TYPE 92 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      3    0
  C3ORF70 WILD-TYPE   92   44
   clus
vv  C3ORF70 MUTATED C3ORF70 WILD-TYPE
  0               3                92
  1               0                44
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    2  0
  C3ORF70 WILD-TYPE 77  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      2    0
  C3ORF70 WILD-TYPE   77    4
   clus
vv  C3ORF70 MUTATED C3ORF70 WILD-TYPE
  0               2                77
  1               0                 4
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    1  2
  C3ORF70 WILD-TYPE 39 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      1    2
  C3ORF70 WILD-TYPE   39   50
     clus
vv    C3ORF70 MUTATED C3ORF70 WILD-TYPE
  NO                1                39
  YES               2                50
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  C3ORF70 MUTATED               0                                3
  C3ORF70 WILD-TYPE             4                              155
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  C3ORF70 MUTATED                                               0
  C3ORF70 WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  C3ORF70 MUTATED                                     1
  C3ORF70 WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  C3ORF70 MUTATED                                           0
  C3ORF70 WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  C3ORF70 MUTATED                                              0
  C3ORF70 WILD-TYPE                                            4
D17V7, multiclass
                                               clus
vv                                              C3ORF70 MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            3
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              C3ORF70 WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                56 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KL        TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-Q1-A73Q 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V9, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                2               119 
       TCGA-EX-A69M        TCGA-FU-A3TX        TCGA-BI-A0VR        TCGA-BI-A0VS 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM        TCGA-C5-A1M5 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MJ        TCGA-C5-A1MP 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MQ        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A3HF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7UC 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-DG-A2KH        TCGA-DG-A2KJ        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KL        TCGA-DG-A2KM        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A1OA        TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HT        TCGA-EA-A3HU 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5FO        TCGA-EA-A5O9        TCGA-EA-A6QX 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2RA        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A1H6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-FU-A23K        TCGA-FU-A23L 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3NI        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JX-A3PZ        TCGA-JX-A3Q8        TCGA-JX-A5QV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-LP-A4AX        TCGA-LP-A5U2        TCGA-LP-A7HU        TCGA-MU-A51Y 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF70 MUTATED                                  0     1
  C3ORF70 WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  C3ORF70 MUTATED                           0
  C3ORF70 WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C3ORF70 MUTATED                                           0     3
  C3ORF70 WILD-TYPE                                         1   135
D17V10, multiclass
                                           clus
vv                                          C3ORF70 MUTATED C3ORF70 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               0                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               135
[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"
D17V11, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     1   3
  C3ORF70 WILD-TYPE  13 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      1    3
  C3ORF70 WILD-TYPE   13  132
                        clus
vv                       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO               3               132
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     3   0
  C3ORF70 WILD-TYPE 136  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      3    0
  C3ORF70 WILD-TYPE  136   45
            clus
vv           C3ORF70 MUTATED C3ORF70 WILD-TYPE
  TUMOR FREE               3               136
  WITH TUMOR               0                45
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  C3ORF70 MUTATED    1  0  2  0  1
  C3ORF70 WILD-TYPE 13 88 80  1  7
D17V14, multiclass
    clus
vv   C3ORF70 MUTATED C3ORF70 WILD-TYPE
  G1               1                13
  G2               0                88
  G3               2                80
  G4               0                 1
  GX               1                 7
[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"
D17V15, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                28 
       TCGA-EX-A69M        TCGA-FU-A3TX        TCGA-BI-A0VR        TCGA-C5-A1BJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BQ        TCGA-C5-A1ME        TCGA-C5-A1MF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MH        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A7CM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3WB        TCGA-HM-A3JK        TCGA-HM-A4S6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JX-A3Q0 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-Q1-A73S        TCGA-RA-A741        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V16, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                56 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KL        TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-Q1-A73Q 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V17, continuous
D17V18, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                51 
       TCGA-FU-A3TX        TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-Q1-A73Q        TCGA-Q1-A73S 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V19, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    0  0
  C3ORF70 WILD-TYPE 26  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      0    0
  C3ORF70 WILD-TYPE   26    3
D17V20, continuous
D17V21, continuous
D17V22, continuous
D17V23, continuous
D17V24, continuous
D17V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  C3ORF70 MUTATED                                     0
  C3ORF70 WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  C3ORF70 MUTATED                                     0                       0
  C3ORF70 WILD-TYPE                                   7                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  C3ORF70 MUTATED                         0                       0
  C3ORF70 WILD-TYPE                       1                       8
D17V26, multiclass
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  C3ORF70 MUTATED                                               0
  C3ORF70 WILD-TYPE                                             3
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  C3ORF70 MUTATED                                                0
  C3ORF70 WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  C3ORF70 MUTATED                                                                                   1
  C3ORF70 WILD-TYPE                                                                                59
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  C3ORF70 MUTATED                                                                                              2
  C3ORF70 WILD-TYPE                                                                                           86
D17V27, multiclass
                                                                                              clus
vv                                                                                             C3ORF70 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               2
                                                                                              clus
vv                                                                                             C3ORF70 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V28, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    1  3
  C3ORF70 WILD-TYPE 62 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      1    3
  C3ORF70 WILD-TYPE   62   64
         clus
vv        C3ORF70 MUTATED C3ORF70 WILD-TYPE
  ABSENT                1                62
  PRESENT               3                64
[1] 2 2
[1] FALSE
D17V29, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                2               119 
       TCGA-EX-A69M        TCGA-FU-A3TX        TCGA-BI-A0VR        TCGA-BI-A0VS 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM        TCGA-C5-A1M5 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MJ        TCGA-C5-A1MP 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MQ        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A3HF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7UC 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-DG-A2KH        TCGA-DG-A2KJ        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KL        TCGA-DG-A2KM        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A1OA        TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HT        TCGA-EA-A3HU 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5FO        TCGA-EA-A5O9        TCGA-EA-A6QX 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2RA        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A1H6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-FU-A23K        TCGA-FU-A23L 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3NI        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JX-A3PZ        TCGA-JX-A3Q8        TCGA-JX-A5QV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-LP-A4AX        TCGA-LP-A5U2        TCGA-LP-A7HU        TCGA-MU-A51Y 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V30, continuous
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                2               138 
       TCGA-EK-A2GZ        TCGA-EX-A69M        TCGA-FU-A3TX        TCGA-BI-A0VR 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-BI-A0VS        TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1BF        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-C5-A1MQ        TCGA-C5-A2LS        TCGA-C5-A2LT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7UC        TCGA-C5-A7UE        TCGA-DG-A2KH        TCGA-DG-A2KJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DG-A2KM        TCGA-DR-A0ZL 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A1OA        TCGA-DS-A3LQ        TCGA-DS-A5RQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3HU        TCGA-EA-A3QD        TCGA-EA-A3QE        TCGA-EA-A3Y4 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A43B        TCGA-EA-A44S 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5FO 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A6QX        TCGA-EK-A2IP        TCGA-EK-A2PK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2R7        TCGA-EK-A2R8        TCGA-EK-A2R9        TCGA-EK-A2RA 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2RC        TCGA-EK-A2RD        TCGA-EK-A2RE        TCGA-EK-A2RJ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2RK        TCGA-EK-A2RL        TCGA-EK-A2RM        TCGA-EK-A2RN 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EK-A3GJ        TCGA-EX-A1H5        TCGA-EX-A1H6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-FU-A23K        TCGA-FU-A23L 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3NI        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JX-A3PZ        TCGA-JX-A3Q8 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JX-A5QV        TCGA-LP-A4AV        TCGA-LP-A4AW        TCGA-LP-A4AX 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-LP-A5U2        TCGA-LP-A7HU        TCGA-MU-A51Y        TCGA-MU-A5YI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV        TCGA-Q1-A73P 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741        TCGA-UC-A7PD 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-UC-A7PF        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V31, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    0  2
  C3ORF70 WILD-TYPE 39 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      0    2
  C3ORF70 WILD-TYPE   39   84
                                          clus
vv                                         C3ORF70 MUTATED C3ORF70 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   0                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2                84
[1] 2 2
[1] FALSE
D17V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  C3ORF70 MUTATED              1           0          0
  C3ORF70 WILD-TYPE            7          43         46
D17V33, multiclass
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                96 
       TCGA-EX-A69M        TCGA-C5-A1BI        TCGA-C5-A1BL        TCGA-C5-A1BN 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1M6        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MN        TCGA-C5-A2LT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HL        TCGA-C5-A7CG 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-DG-A2KM        TCGA-DR-A0ZL 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A1OA        TCGA-DS-A3LQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HT        TCGA-EA-A3HU 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3QE        TCGA-EA-A410        TCGA-EA-A411 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZE        TCGA-EA-A5ZF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2R7        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EX-A69L        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A57G        TCGA-FU-A770 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-HM-A6W2 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JX-A3PZ        TCGA-JX-A3Q0        TCGA-JX-A3Q8 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JX-A5QV        TCGA-LP-A5U2        TCGA-LP-A5U3        TCGA-LP-A7HU 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A5R1        TCGA-Q1-A5R2        TCGA-Q1-A5R3        TCGA-Q1-A6DV 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-Q1-A73S        TCGA-UC-A7PD        TCGA-WL-A834 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
D17V34, continuous
D17V35, binary
                   cls
clus                 0  1
  C3ORF70 MUTATED    2  2
  C3ORF70 WILD-TYPE 86 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      2    2
  C3ORF70 WILD-TYPE   86   14
         clus
vv        C3ORF70 MUTATED C3ORF70 WILD-TYPE
  ABSENT                2                86
  PRESENT               2                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  C3ORF70 MUTATED             0         1     0
  C3ORF70 WILD-TYPE           4        52     1
D17V36, multiclass
[1] "Remove cluster labels:" "C3ORF70 MUTATED"       
clus
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                1                57 
       TCGA-C5-A1BE        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1BQ 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A1MQ        TCGA-C5-A2LT        TCGA-C5-A2LX 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A3HD        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-C5-A7UE 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-DG-A2KJ        TCGA-DG-A2KK 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DG-A2KM        TCGA-DR-A0ZM        TCGA-DS-A0VM        TCGA-DS-A0VN 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A1OA        TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A4BA        TCGA-EK-A2H0 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-EK-A2H1        TCGA-HM-A3JJ        TCGA-HM-A6W2        TCGA-IR-A3LA 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-JW-A5VG        TCGA-JW-A5VH        TCGA-JW-A5VI 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-JW-A852        TCGA-LP-A4AU        TCGA-Q1-A5R2        TCGA-Q1-A5R3 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-Q1-A73O        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-R2-A69V 
"C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" "C3ORF70 WILD-TYPE" 
       TCGA-RA-A741 
"C3ORF70 WILD-TYPE" 
D17V37, continuous
D17V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  C3ORF70 MUTATED         1        0         0         0        0         1
  C3ORF70 WILD-TYPE       3        1         1         1       28        52
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  C3ORF70 MUTATED           0        0         0          1          0
  C3ORF70 WILD-TYPE        29        4         6          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  C3ORF70 MUTATED           1         0          0         0         0
  C3ORF70 WILD-TYPE        13         1         29         2         5
D17V39, multiclass
            clus
vv           C3ORF70 MUTATED C3ORF70 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 0                28
  STAGE IB1                1                52
  STAGE IB2                0                29
  STAGE II                 0                 4
  STAGE IIA                0                 6
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                1                13
  STAGE III                0                 1
  STAGE IIIB               0                29
  STAGE IVA                0                 2
  STAGE IVB                0                 5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = BAP1 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED     3   1
  BAP1 WILD-TYPE 147  41
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            188 
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             41 
$`BAP1 MUTATED`
TCGA-C5-A1BM TCGA-EA-A44S TCGA-EK-A2RB TCGA-EK-A2RC 
       82.85        12.13         0.30         4.24 

$`BAP1 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       58.88        36.76        55.63       117.99       118.65        28.90 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
       40.87        37.35        30.90        31.36        33.30        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
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-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
        6.64         1.51        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE 
        0.89         1.45         0.13        40.96         0.07         1.87 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        1.74         0.43        47.77         1.64         2.33         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.49         0.89        20.35         7.92        15.22 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79        12.23        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       35.44        10.55         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89        12.49         0.30         0.82        13.35        28.08 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       34.62        54.81        35.05        20.84        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.30           0.07 
  BAP1 MUTATED BAP1 WILD-TYPE 
         82.85         210.67 
  BAP1 MUTATED BAP1 WILD-TYPE 
         8.185         23.920 
[1] "0.3 - 82.8 (8.2)"   "0.1 - 210.7 (23.9)"
[1] "hr=" "1.7"
D18V2, continuous
                vv
clus              T1  T2 T3+T4
  BAP1 MUTATED     0   2     0
  BAP1 WILD-TYPE 104  38     5
D18V3, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            147 
    TCGA-EX-A449     TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M1     TCGA-C5-A3HE     TCGA-C5-A3HL     TCGA-C5-A7CG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-DG-A2KH     TCGA-DG-A2KJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR     TCGA-EA-A3HT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439     TCGA-EA-A43B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-EA-A5ZD     TCGA-EA-A5ZE     TCGA-EA-A5ZF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A6QX     TCGA-EA-A78R     TCGA-EK-A2IP     TCGA-EK-A2R7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2R8     TCGA-EK-A2R9     TCGA-EK-A2RA     TCGA-EK-A2RD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RE     TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A3GJ     TCGA-EK-A3GK     TCGA-EX-A1H5 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L     TCGA-FU-A23K 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ     TCGA-FU-A3WB 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3YQ     TCGA-FU-A40J     TCGA-FU-A57G     TCGA-FU-A5XV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852     TCGA-JX-A3PZ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A4AU 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AV     TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A5U3     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A6DV     TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V4, binary
                cls
clus              0  1
  BAP1 MUTATED    0  2
  BAP1 WILD-TYPE 95 42
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    2
  BAP1 WILD-TYPE   95   42
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            0             95
  1            2             42
[1] 2 2
[1] FALSE
D18V5, binary
                cls
clus              0  1
  BAP1 MUTATED    1  0
  BAP1 WILD-TYPE 78  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    0
  BAP1 WILD-TYPE   78    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            1             78
  1            0              4
[1] 2 2
[1] FALSE
D18V6, binary
                cls
clus              0  1
  BAP1 MUTATED    0  0
  BAP1 WILD-TYPE 40 52
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    0
  BAP1 WILD-TYPE   40   52
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  BAP1 MUTATED               0                                4
  BAP1 WILD-TYPE             4                              154
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  BAP1 MUTATED                                               0
  BAP1 WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  BAP1 MUTATED                                     0
  BAP1 WILD-TYPE                                  21
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  BAP1 MUTATED                                           0
  BAP1 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  BAP1 MUTATED                                              0
  BAP1 WILD-TYPE                                            4
D18V7, multiclass
                                               clus
vv                                              BAP1 MUTATED BAP1 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         4            154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, continuous
D18V9, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            119 
    TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-BI-A0VS 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1M5     TCGA-C5-A1M7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A3HF     TCGA-C5-A3HL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-EA-A6QX     TCGA-EK-A2RA     TCGA-EK-A2RO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A4AX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A5U2     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A6DV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     0
  BAP1 WILD-TYPE                                8    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  BAP1 MUTATED                           1
  BAP1 WILD-TYPE                        15
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAP1 MUTATED                                           0     2
  BAP1 WILD-TYPE                                         1   136
D18V10, multiclass
                                           clus
vv                                          BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              8
  ASIAN                                                0             19
  BLACK OR AFRICAN AMERICAN                            1             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            136
[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"
D18V11, binary
                cls
clus               0   1
  BAP1 MUTATED     0   2
  BAP1 WILD-TYPE  14 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    2
  BAP1 WILD-TYPE   14  133
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            2            133
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                cls
clus               0   1
  BAP1 MUTATED     4   0
  BAP1 WILD-TYPE 135  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      4    0
  BAP1 WILD-TYPE  135   45
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  TUMOR FREE            4            135
  WITH TUMOR            0             45
[1] 2 2
[1] FALSE
                vv
clus             G1 G2 G3 G4 GX
  BAP1 MUTATED    0  2  2  0  0
  BAP1 WILD-TYPE 14 86 80  1  8
D18V14, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  G1            0             14
  G2            2             86
  G3            2             80
  G4            0              1
  GX            0              8
[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"
D18V15, continuous
D18V16, continuous
D18V17, continuous
D18V18, continuous
D18V19, binary
                cls
clus              0  1
  BAP1 MUTATED    1  0
  BAP1 WILD-TYPE 25  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    0
  BAP1 WILD-TYPE   25    3
                         clus
vv                        BAP1 MUTATED BAP1 WILD-TYPE
  COMPLETED AS PLANNED               1             25
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
D18V20, continuous
D18V21, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             99 
    TCGA-EX-A449     TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A556 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A770     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-IR-A3L7     TCGA-IR-A3LC     TCGA-IR-A3LF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V22, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            108 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A5RQ     TCGA-DS-A7WF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HQ     TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A411     TCGA-EA-A556     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2IP     TCGA-EK-A2RK     TCGA-EX-A69L     TCGA-FU-A2QG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7     TCGA-IR-A3LC 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V23, continuous
D18V24, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            107 
    TCGA-EX-A449     TCGA-BI-A0VS     TCGA-C5-A0TN     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A556     TCGA-EA-A5O9     TCGA-EA-A6QX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EX-A1H6     TCGA-FU-A2QG     TCGA-FU-A3EO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A770 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-IR-A3L7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A69B     TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-MU-A51Y 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V25, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            101 
    TCGA-EX-A69M     TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A556 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A5XV     TCGA-FU-A770 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JK     TCGA-IR-A3L7     TCGA-IR-A3LC 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-Q1-A73Q     TCGA-RA-A741     TCGA-UC-A7PD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PF 
"BAP1 WILD-TYPE" 
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  BAP1 MUTATED                                     0
  BAP1 WILD-TYPE                                   1
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  BAP1 MUTATED                                     0                       0
  BAP1 WILD-TYPE                                   7                      30
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  BAP1 MUTATED                         0                       2
  BAP1 WILD-TYPE                       1                       6
D18V26, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             45 
    TCGA-EX-A449     TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2M1     TCGA-C5-A3HE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-EA-A50E     TCGA-EK-A2RK     TCGA-EK-A2RN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A3EO     TCGA-HM-A4S6     TCGA-IR-A3LH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-MU-A51Y     TCGA-UC-A7PD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-WL-A834 
"BAP1 WILD-TYPE" 
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  BAP1 MUTATED                                               0
  BAP1 WILD-TYPE                                             3
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  BAP1 MUTATED                                                0
  BAP1 WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  BAP1 MUTATED                                                                                   1
  BAP1 WILD-TYPE                                                                                59
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  BAP1 MUTATED                                                                                              1
  BAP1 WILD-TYPE                                                                                           87
D18V27, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            159 
    TCGA-EK-A2GZ     TCGA-EX-A449     TCGA-EX-A69M     TCGA-FU-A3TX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A0TN     TCGA-C5-A1BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CO     TCGA-DG-A2KH     TCGA-DG-A2KK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KL     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A439     TCGA-EA-A43B     TCGA-EA-A4BA     TCGA-EA-A50E 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2PG     TCGA-EK-A2PK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2RD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RE     TCGA-EK-A2RK     TCGA-EK-A2RN     TCGA-EK-A2RO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A3GM     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3YQ     TCGA-FU-A40J     TCGA-FU-A57G 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA     TCGA-HM-A3JJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AU     TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A5U3     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DT     TCGA-Q1-A6DV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73P     TCGA-Q1-A73Q 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73R     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V28, binary
                cls
clus              0  1
  BAP1 MUTATED    1  2
  BAP1 WILD-TYPE 62 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    2
  BAP1 WILD-TYPE   62   65
         clus
vv        BAP1 MUTATED BAP1 WILD-TYPE
  ABSENT             1             62
  PRESENT            2             65
[1] 2 2
[1] FALSE
D18V29, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            119 
    TCGA-EX-A69M     TCGA-FU-A3TX     TCGA-BI-A0VR     TCGA-BI-A0VS 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1M5     TCGA-C5-A1M7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A3HF     TCGA-C5-A3HL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-C5-A7UE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-EA-A6QX     TCGA-EK-A2RA     TCGA-EK-A2RO 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A4AX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A5U2     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A6DV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V30, continuous
D18V31, binary
                cls
clus              0  1
  BAP1 MUTATED    0  2
  BAP1 WILD-TYPE 39 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    2
  BAP1 WILD-TYPE   39   84
                                          clus
vv                                         BAP1 MUTATED BAP1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                0             39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            2             84
[1] 2 2
[1] FALSE
D18V32, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  BAP1 MUTATED              0           0          1
  BAP1 WILD-TYPE            8          43         45
D18V33, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             96 
    TCGA-EX-A69M     TCGA-C5-A1BI     TCGA-C5-A1BL     TCGA-C5-A1BN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MN     TCGA-C5-A2LT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HL     TCGA-C5-A7CG 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KM     TCGA-DR-A0ZL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A7WF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3HQ     TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A410     TCGA-EA-A411 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5O9     TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EK-A2R7 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JW-A69B     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-UC-A7PD     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D18V34, continuous
D18V35, binary
                cls
clus              0  1
  BAP1 MUTATED    1  1
  BAP1 WILD-TYPE 87 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    1
  BAP1 WILD-TYPE   87   15
         clus
vv        BAP1 MUTATED BAP1 WILD-TYPE
  ABSENT             1             87
  PRESENT            1             15
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  BAP1 MUTATED             0         0     0
  BAP1 WILD-TYPE           4        53     1
D18V36, multiclass
D18V37, continuous
D18V38, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  BAP1 MUTATED         0        0         0         0        1         1
  BAP1 WILD-TYPE       4        1         1         1       27        52
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  BAP1 MUTATED           0        0         0          0          0         0
  BAP1 WILD-TYPE        29        4         6          5          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  BAP1 MUTATED           0          1         0         1
  BAP1 WILD-TYPE         1         28         2         4
D18V39, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              1             27
  STAGE IB1             1             52
  STAGE IB2             0             29
  STAGE II              0              4
  STAGE IIA             0              6
  STAGE IIA1            0              5
  STAGE IIA2            0              7
  STAGE IIB             0             14
  STAGE III             0              1
  STAGE IIIB            1             28
  STAGE IVA             0              2
  STAGE IVB             1              4
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = USP28 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED     2   2
  USP28 WILD-TYPE 148  40
  USP28 MUTATED USP28 WILD-TYPE 
              4             188 
  USP28 MUTATED USP28 WILD-TYPE 
              2              40 
$`USP28 MUTATED`
TCGA-C5-A1BQ TCGA-DS-A0VM TCGA-IR-A3LA TCGA-IR-A3LK 
       19.86       117.99       137.16        29.85 

$`USP28 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       58.88        36.76        55.63       118.65        28.90        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.36        33.30        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01        12.13 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
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-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
        6.64         1.51        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.89         1.45         0.13        40.96         0.30         4.24 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         1.87         1.74         0.43        47.77         1.64 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.33         0.07         0.10         0.49         0.89        20.35 
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-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       28.31        14.01        35.44        10.55         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       21.67        20.78        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89        12.49         0.30         0.82        13.35        28.08 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       34.62        54.81        35.05        20.84        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  USP28 MUTATED USP28 WILD-TYPE 
          19.86            0.07 
  USP28 MUTATED USP28 WILD-TYPE 
         137.16          210.67 
  USP28 MUTATED USP28 WILD-TYPE 
         73.920          23.325 
[1] "19.9 - 137.2 (73.9)" "0.1 - 210.7 (23.3)" 
[1] "hr=" "1.1"
D19V2, continuous
                 vv
clus               T1  T2 T3+T4
  USP28 MUTATED     3   0     0
  USP28 WILD-TYPE 101  40     5
D19V3, multiclass
       clus
vv      USP28 MUTATED USP28 WILD-TYPE
  T1                3             101
  T2                0              40
  T3+T4             0               5
[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"
D19V4, binary
                 cls
clus               0  1
  USP28 MUTATED    2  1
  USP28 WILD-TYPE 93 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      2    1
  USP28 WILD-TYPE   93   43
   clus
vv  USP28 MUTATED USP28 WILD-TYPE
  0             2              93
  1             1              43
[1] 2 2
[1] FALSE
D19V5, binary
                 cls
clus               0  1
  USP28 MUTATED    3  0
  USP28 WILD-TYPE 76  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3    0
  USP28 WILD-TYPE   76    4
   clus
vv  USP28 MUTATED USP28 WILD-TYPE
  0             3              76
  1             0               4
[1] 2 2
[1] FALSE
D19V6, binary
                 cls
clus               0  1
  USP28 MUTATED    1  2
  USP28 WILD-TYPE 39 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      1    2
  USP28 WILD-TYPE   39   50
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO              1              39
  YES             2              50
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  USP28 MUTATED               0                                3
  USP28 WILD-TYPE             4                              155
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  USP28 MUTATED                                               0
  USP28 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  USP28 MUTATED                                     0
  USP28 WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  USP28 MUTATED                                           1
  USP28 WILD-TYPE                                         1
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  USP28 MUTATED                                              0
  USP28 WILD-TYPE                                            4
D19V7, multiclass
                                               clus
vv                                              USP28 MUTATED USP28 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          3             155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 1               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
D19V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP28 MUTATED                                  0     0
  USP28 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  USP28 MUTATED                           0
  USP28 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP28 MUTATED                                           0     4
  USP28 WILD-TYPE                                         1   134
D19V10, multiclass
                                           clus
vv                                          USP28 MUTATED USP28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 0              19
  BLACK OR AFRICAN AMERICAN                             0              16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             134
[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"
D19V11, binary
                 cls
clus                0   1
  USP28 MUTATED     0   2
  USP28 WILD-TYPE  14 133
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    2
  USP28 WILD-TYPE   14  133
                        clus
vv                       USP28 MUTATED USP28 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             2             133
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                 cls
clus                0   1
  USP28 MUTATED     3   1
  USP28 WILD-TYPE 136  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3    1
  USP28 WILD-TYPE  136   44
            clus
vv           USP28 MUTATED USP28 WILD-TYPE
  TUMOR FREE             3             136
  WITH TUMOR             1              44
[1] 2 2
[1] FALSE
                 vv
clus              G1 G2 G3 G4 GX
  USP28 MUTATED    0  1  3  0  0
  USP28 WILD-TYPE 14 87 79  1  8
D19V14, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  G1             0              14
  G2             1              87
  G3             3              79
  G4             0               1
  GX             0               8
[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"
D19V15, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              28 
     TCGA-EX-A69M      TCGA-FU-A3TX      TCGA-BI-A0VR      TCGA-C5-A1BJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A7CM      TCGA-C5-A7CO 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DS-A3LQ      TCGA-EK-A2RA      TCGA-FU-A2QG 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JX-A3Q0      TCGA-MU-A5YI 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-Q1-A6DW      TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
D19V16, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
D19V17, continuous
D19V18, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              51 
     TCGA-FU-A3TX      TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A2LS      TCGA-C5-A2LT 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DR-A0ZM 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV      TCGA-FU-A770 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LB 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK      TCGA-JX-A3Q0 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
D19V19, binary
                 cls
clus               0  1
  USP28 MUTATED    0  0
  USP28 WILD-TYPE 26  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    0
  USP28 WILD-TYPE   26    3
D19V20, continuous
D19V21, continuous
D19V22, continuous
D19V23, continuous
D19V24, continuous
D19V25, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  USP28 MUTATED                                     0
  USP28 WILD-TYPE                                   1
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  USP28 MUTATED                                     1                       1
  USP28 WILD-TYPE                                   6                      29
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  USP28 MUTATED                         0                       0
  USP28 WILD-TYPE                       1                       8
D19V26, multiclass
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              2              45 
     TCGA-EX-A449      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DR-A0ZM 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VN      TCGA-DS-A1OA 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-EA-A50E      TCGA-EK-A2RC      TCGA-EK-A2RK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EX-A1H5      TCGA-FU-A3EO      TCGA-HM-A4S6 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-MU-A51Y      TCGA-UC-A7PD 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-WL-A834 
"USP28 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  USP28 MUTATED                                               0
  USP28 WILD-TYPE                                             3
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  USP28 MUTATED                                                0
  USP28 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  USP28 MUTATED                                                                                   4
  USP28 WILD-TYPE                                                                                56
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  USP28 MUTATED                                                                                              0
  USP28 WILD-TYPE                                                                                           88
D19V27, multiclass
                                                                                              clus
vv                                                                                             USP28 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                           0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                        4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             0
                                                                                              clus
vv                                                                                             USP28 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V28, binary
                 cls
clus               0  1
  USP28 MUTATED    0  2
  USP28 WILD-TYPE 63 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    2
  USP28 WILD-TYPE   63   65
         clus
vv        USP28 MUTATED USP28 WILD-TYPE
  ABSENT              0              63
  PRESENT             2              65
[1] 2 2
[1] FALSE
D19V29, continuous
D19V30, continuous
D19V31, binary
                 cls
clus               0  1
  USP28 MUTATED    1  1
  USP28 WILD-TYPE 38 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      1    1
  USP28 WILD-TYPE   38   85
                                          clus
vv                                         USP28 MUTATED USP28 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 1              38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             1              85
[1] 2 2
[1] FALSE
D19V32, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  USP28 MUTATED              0           1          2
  USP28 WILD-TYPE            8          42         44
D19V33, multiclass
              clus
vv             USP28 MUTATED USP28 WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              1              42
  NEVER USED               2              44
[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"
D19V34, continuous
D19V35, binary
                 cls
clus               0  1
  USP28 MUTATED    3  0
  USP28 WILD-TYPE 85 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3    0
  USP28 WILD-TYPE   85   16
         clus
vv        USP28 MUTATED USP28 WILD-TYPE
  ABSENT              3              85
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  USP28 MUTATED             0         3     0
  USP28 WILD-TYPE           4        50     1
D19V36, multiclass
             clus
vv            USP28 MUTATED USP28 WILD-TYPE
  CARBOPLATIN             0               4
  CISPLATIN               3              50
  OTHER                   0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V37, continuous
D19V38, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  USP28 MUTATED         0        0         0         0        1         1
  USP28 WILD-TYPE       4        1         1         1       27        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  USP28 MUTATED           1        0         0          0          0         0
  USP28 WILD-TYPE        28        4         6          5          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  USP28 MUTATED           0          1         0         0
  USP28 WILD-TYPE         1         28         2         5
D19V39, multiclass
            clus
vv           USP28 MUTATED USP28 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              1              52
  STAGE IB2              1              28
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              0              14
  STAGE III              0               1
  STAGE IIIB             1              28
  STAGE IVA              0               2
  STAGE IVB              0               5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = IFNGR1 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  IFNGR1 MUTATED     5   1
  IFNGR1 WILD-TYPE 145  41
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              186 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               1               41 
$`IFNGR1 MUTATED`
TCGA-C5-A1BL TCGA-C5-A2M2 TCGA-C5-A7UH TCGA-FU-A3HZ TCGA-JW-A5VJ TCGA-LP-A5U2 
      173.29        33.24       131.11        36.26        21.44         0.30 

$`IFNGR1 WILD-TYPE`
TCGA-EK-A2GZ TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A3TX TCGA-BI-A0VR TCGA-BI-A0VS 
       12.59        14.70         8.32         1.48        49.48        57.04 
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       33.90        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ 
      147.35        17.19       155.77         9.34         1.12        95.11 
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-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
       55.63       117.99       118.65        28.90        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
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-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01        12.13        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        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-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        1.51        19.27         0.39         0.43         0.59         0.89 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        40.96         0.30         4.24         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        1.87         1.74         0.43        47.77         1.64         2.33 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.49         0.89        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       15.22        19.79        12.23        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       31.36        20.98        26.14        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       35.44        10.55         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        20.48        15.58        28.37         8.28 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
       12.49         0.82        13.35        28.08        34.62        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       35.05        20.84        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       22.62        19.59        14.60        11.67        93.99        26.01 

  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
            0.30             0.07 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
          173.29           210.67 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
          34.750           23.325 
[1] "0.3 - 173.3 (34.8)" "0.1 - 210.7 (23.3)"
[1] "hr=" "2.2"
D20V2, continuous
                  vv
clus                T1  T2 T3+T4
  IFNGR1 MUTATED     0   3     0
  IFNGR1 WILD-TYPE 104  37     5
D20V3, multiclass
       clus
vv      IFNGR1 MUTATED IFNGR1 WILD-TYPE
  T1                 0              104
  T2                 3               37
  T3+T4              0                5
[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"
D20V4, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    1  1
  IFNGR1 WILD-TYPE 94 43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    1
  IFNGR1 WILD-TYPE   94   43
   clus
vv  IFNGR1 MUTATED IFNGR1 WILD-TYPE
  0              1               94
  1              1               43
[1] 2 2
[1] FALSE
D20V5, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    1  0
  IFNGR1 WILD-TYPE 78  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    0
  IFNGR1 WILD-TYPE   78    4
   clus
vv  IFNGR1 MUTATED IFNGR1 WILD-TYPE
  0              1               78
  1              0                4
[1] 2 2
[1] FALSE
D20V6, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    2  1
  IFNGR1 WILD-TYPE 38 51
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      2    1
  IFNGR1 WILD-TYPE   38   51
     clus
vv    IFNGR1 MUTATED IFNGR1 WILD-TYPE
  NO               2               38
  YES              1               51
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  IFNGR1 MUTATED               0                                4
  IFNGR1 WILD-TYPE             4                              154
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  IFNGR1 MUTATED                                               1
  IFNGR1 WILD-TYPE                                             4
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  IFNGR1 MUTATED                                     1
  IFNGR1 WILD-TYPE                                  20
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  IFNGR1 MUTATED                                           0
  IFNGR1 WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  IFNGR1 MUTATED                                              0
  IFNGR1 WILD-TYPE                                            4
D20V7, multiclass
                                               clus
vv                                              IFNGR1 MUTATED IFNGR1 WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           4              154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              1                4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        1               20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A3HD       TCGA-C5-A3HF 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CO 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DR-A0ZM 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D20V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNGR1 MUTATED                                  1     1
  IFNGR1 WILD-TYPE                                7    18
                  vv
clus               BLACK OR AFRICAN AMERICAN
  IFNGR1 MUTATED                           0
  IFNGR1 WILD-TYPE                        16
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFNGR1 MUTATED                                           0     4
  IFNGR1 WILD-TYPE                                         1   134
D20V10, multiclass
                                           clus
vv                                          IFNGR1 MUTATED IFNGR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                7
  ASIAN                                                  1               18
  BLACK OR AFRICAN AMERICAN                              0               16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              134
[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"
D20V11, binary
                  cls
clus                 0   1
  IFNGR1 MUTATED     1   5
  IFNGR1 WILD-TYPE  13 130
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    5
  IFNGR1 WILD-TYPE   13  130
                        clus
vv                       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO              5              130
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                  cls
clus                 0   1
  IFNGR1 MUTATED     4   1
  IFNGR1 WILD-TYPE 135  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      4    1
  IFNGR1 WILD-TYPE  135   44
            clus
vv           IFNGR1 MUTATED IFNGR1 WILD-TYPE
  TUMOR FREE              4              135
  WITH TUMOR              1               44
[1] 2 2
[1] FALSE
                  vv
clus               G1 G2 G3 G4 GX
  IFNGR1 MUTATED    0  2  4  0  0
  IFNGR1 WILD-TYPE 14 86 78  1  8
D20V14, multiclass
    clus
vv   IFNGR1 MUTATED IFNGR1 WILD-TYPE
  G1              0               14
  G2              2               86
  G3              4               78
  G4              0                1
  GX              0                8
[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"
D20V15, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               27 
      TCGA-EX-A69M       TCGA-FU-A3TX       TCGA-BI-A0VR       TCGA-C5-A1BJ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-DG-A2KK 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-EK-A2RA       TCGA-FU-A2QG       TCGA-FU-A3WB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-IR-A3L7       TCGA-IR-A3LB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JX-A3Q0       TCGA-MU-A5YI       TCGA-Q1-A6DW 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D20V16, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A3HD       TCGA-C5-A3HF 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CO 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DR-A0ZM 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D20V17, continuous
D20V18, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               50 
      TCGA-FU-A3TX       TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A2LS       TCGA-C5-A2LT 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A3HD 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CL       TCGA-C5-A7CO 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DR-A0ZM       TCGA-DS-A5RQ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-EA-A556       TCGA-EK-A2RA       TCGA-EX-A1H5       TCGA-FU-A2QG 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ       TCGA-FU-A3WB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770       TCGA-HM-A4S6 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB       TCGA-IR-A3LH 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0       TCGA-MU-A5YI 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S       TCGA-RA-A741 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D20V19, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    1  0
  IFNGR1 WILD-TYPE 25  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    0
  IFNGR1 WILD-TYPE   25    3
                         clus
vv                        IFNGR1 MUTATED IFNGR1 WILD-TYPE
  COMPLETED AS PLANNED                 1               25
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
D20V20, continuous
D20V21, continuous
D20V22, continuous
D20V23, continuous
D20V24, continuous
D20V25, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  IFNGR1 MUTATED                                     0
  IFNGR1 WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  IFNGR1 MUTATED                                     0                       0
  IFNGR1 WILD-TYPE                                   7                      30
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  IFNGR1 MUTATED                         0                       0
  IFNGR1 WILD-TYPE                       1                       8
D20V26, multiclass
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  IFNGR1 MUTATED                                               0
  IFNGR1 WILD-TYPE                                             3
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  IFNGR1 MUTATED                                                0
  IFNGR1 WILD-TYPE                                             10
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  IFNGR1 MUTATED                                                                                   3
  IFNGR1 WILD-TYPE                                                                                57
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  IFNGR1 MUTATED                                                                                              2
  IFNGR1 WILD-TYPE                                                                                           86
D20V27, multiclass
                                                                                              clus
vv                                                                                             IFNGR1 MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              2
                                                                                              clus
vv                                                                                             IFNGR1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               3
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V28, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    0  3
  IFNGR1 WILD-TYPE 63 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      0    3
  IFNGR1 WILD-TYPE   63   64
         clus
vv        IFNGR1 MUTATED IFNGR1 WILD-TYPE
  ABSENT               0               63
  PRESENT              3               64
[1] 2 2
[1] FALSE
D20V29, continuous
D20V30, continuous
D20V31, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    0  3
  IFNGR1 WILD-TYPE 39 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      0    3
  IFNGR1 WILD-TYPE   39   83
                                          clus
vv                                         IFNGR1 MUTATED IFNGR1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  0               39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              3               83
[1] 2 2
[1] FALSE
D20V32, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  IFNGR1 MUTATED              0           2          3
  IFNGR1 WILD-TYPE            8          41         43
D20V33, multiclass
              clus
vv             IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CURRENT USER              0                8
  FORMER USER               2               41
  NEVER USED                3               43
[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"
D20V34, continuous
D20V35, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    2  1
  IFNGR1 WILD-TYPE 86 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      2    1
  IFNGR1 WILD-TYPE   86   15
         clus
vv        IFNGR1 MUTATED IFNGR1 WILD-TYPE
  ABSENT               2               86
  PRESENT              1               15
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  IFNGR1 MUTATED             0         2     0
  IFNGR1 WILD-TYPE           4        51     1
D20V36, multiclass
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               56 
      TCGA-C5-A1BE       TCGA-C5-A1BI       TCGA-C5-A1BN       TCGA-C5-A1BQ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1MK 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A1MQ       TCGA-C5-A2LT       TCGA-C5-A2LX 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A2LY       TCGA-C5-A3HD       TCGA-C5-A7CJ       TCGA-C5-A7CK 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-C5-A7UE 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KM 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DR-A0ZM       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DS-A7WI       TCGA-EA-A4BA       TCGA-EK-A2H0       TCGA-EK-A2H1 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-HM-A3JJ       TCGA-HM-A6W2       TCGA-IR-A3LA       TCGA-IR-A3LB 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-JW-A5VG       TCGA-JW-A5VH       TCGA-JW-A5VI       TCGA-JW-A5VK 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-JW-A5VL       TCGA-JW-A69B       TCGA-JW-A852       TCGA-LP-A4AU 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-Q1-A5R2       TCGA-Q1-A5R3       TCGA-Q1-A6DW       TCGA-Q1-A73O 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-Q1-A73Q       TCGA-Q1-A73S       TCGA-R2-A69V       TCGA-RA-A741 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D20V37, continuous
D20V38, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  IFNGR1 MUTATED         0        0         0         0        1         0
  IFNGR1 WILD-TYPE       4        1         1         1       27        53
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  IFNGR1 MUTATED           1        0         0          0          1         1
  IFNGR1 WILD-TYPE        28        4         6          5          6        13
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  IFNGR1 MUTATED           0          2         0         0
  IFNGR1 WILD-TYPE         1         27         2         5
D20V39, multiclass
            clus
vv           IFNGR1 MUTATED IFNGR1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                1               27
  STAGE IB1               0               53
  STAGE IB2               1               28
  STAGE II                0                4
  STAGE IIA               0                6
  STAGE IIA1              0                5
  STAGE IIA2              1                6
  STAGE IIB               1               13
  STAGE III               0                1
  STAGE IIIB              2               27
  STAGE IVA               0                2
  STAGE IVB               0                5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
