[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/15076797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/15165547/transformed.cor.cli.txt"

nPatients in clinical file=304, in cluster file=194, common to both=194
[1]  38 194
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            11            183 
  KRAS MUTATED KRAS 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] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             175 
[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] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
  PTEN MUTATED PTEN WILD-TYPE 
            15            179 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              180 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             185 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
  EP300 MUTATED EP300 WILD-TYPE 
             21             173 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              53              141 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              182 
[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 
              10              184 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              184 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            190 
[1] "RAB35 MUTATION ANALYSIS"
[1] 3
  RAB35 MUTATED RAB35 WILD-TYPE 
              4             190 
  RAB35 MUTATED RAB35 WILD-TYPE 
              4             190 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             11             183 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             11             183 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             187 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             187 
[1] "TCTE1 MUTATION ANALYSIS"
[1] 3
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              5             189 
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              5             189 
[1] "NHS MUTATION ANALYSIS"
[1] 3
  NHS MUTATED NHS WILD-TYPE 
           12           182 
  NHS MUTATED NHS WILD-TYPE 
           12           182 
[1] "LIN9 MUTATION ANALYSIS"
[1] 3
  LIN9 MUTATED LIN9 WILD-TYPE 
             7            187 
  LIN9 MUTATED LIN9 WILD-TYPE 
             7            187 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                190 
[1] "MED1 MUTATION ANALYSIS"
[1] 3
  MED1 MUTATED MED1 WILD-TYPE 
            11            183 
  MED1 MUTATED MED1 WILD-TYPE 
            11            183 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
  USP28 MUTATED USP28 WILD-TYPE 
              4             190 
[1] "IDS MUTATION ANALYSIS"
[1] 3
  IDS MUTATED IDS WILD-TYPE 
            7           187 
  IDS MUTATED IDS WILD-TYPE 
            7           187 
[1] "TRIM9 MUTATION ANALYSIS"
[1] 3
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              8             186 
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              8             186 
[1] "SEMA4B MUTATION ANALYSIS"
[1] 3
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               7              187 
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               7              187 
[1] "ARHGAP4 MUTATION ANALYSIS"
[1] 3
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                6               188 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                6               188 
[1] "POU2F1 MUTATION ANALYSIS"
[1] 3
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               3              191 
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               3              191 
[1] "IFNGR1 MUTATION ANALYSIS"
[1] 3
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              188 
[1] "IGFN1 MUTATION ANALYSIS"
[1] 3
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             11             183 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             11             183 
[1] "RPGR MUTATION ANALYSIS"
[1] 3
  RPGR MUTATED RPGR WILD-TYPE 
             9            185 
  RPGR MUTATED RPGR WILD-TYPE 
             9            185 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             185 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
             4            190 
  GAS6 MUTATED GAS6 WILD-TYPE 
             4            190 
[1] "ABCD1 MUTATION ANALYSIS"
[1] 3
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              7             187 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              7             187 
[1] "RPAP1 MUTATION ANALYSIS"
[1] 3
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              4             190 
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              4             190 
[1] "HIST1H4E MUTATION ANALYSIS"
[1] 3
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 4                190 
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 4                190 
[1] "NLRC5 MUTATION ANALYSIS"
[1] 3
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             187 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             187 
[1] "DDX41 MUTATION ANALYSIS"
[1] 3
  DDX41 MUTATED DDX41 WILD-TYPE 
              5             189 
  DDX41 MUTATED DDX41 WILD-TYPE 
              5             189 
[1] "MCM7 MUTATION ANALYSIS"
[1] 3
  MCM7 MUTATED MCM7 WILD-TYPE 
             3            191 
  MCM7 MUTATED MCM7 WILD-TYPE 
             3            191 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                  
 [2] "VITAL_STATUS"                                    
 [3] "DAYS_TO_DEATH"                                   
 [4] "DAYS_TO_LAST_FOLLOWUP"                           
 [5] "PRIMARY_SITE_OF_DISEASE"                         
 [6] "NEOPLASM_DISEASESTAGE"                           
 [7] "PATHOLOGY_T_STAGE"                               
 [8] "PATHOLOGY_N_STAGE"                               
 [9] "PATHOLOGY_M_STAGE"                               
[10] "DCC_UPLOAD_DATE"                                 
[11] "GENDER"                                          
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"            
[13] "HISTOLOGICAL_TYPE"                               
[14] "RADIATIONS_RADIATION_REGIMENINDICATION"          
[15] "NUMBER_PACK_YEARS_SMOKED"                        
[16] "NUMBER_OF_LYMPH_NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCH_NUMBER"                                    
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASM_HISTOLOGIC_GRADE"                       
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "LYMPH_NODE_LOCATION"                             
[42] "POS_LYMPH_NODE_LOCATION"                         
[43] "MENOPAUSE_STATUS"                                
[44] "LYMPHOVASCULAR_INVOLVEMENT"                      
[45] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[46] "LYMPH_NODES_EXAMINED"                            
[47] "KERATINIZATION_SQUAMOUS_CELL"                    
[48] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[49] "HYSTERECTOMY_TYPE"                               
[50] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[51] "HEIGHT_CM_AT_DIAGNOSIS"                          
[52] "FEDPET_OR_CT_RESULTS"                            
[53] "CORPUS_INVOLVEMENT"                              
[54] "CHEMO_CONCURRENT_TYPE"                           
[55] "CERVIX_SUV_RESULTS"                              
[56] "CAUSE_OF_DEATH"                                  
[57] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[58] "AGE_AT_DIAGNOSIS"                                
[59] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 59 rows and 194 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=144,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH_NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_TREATMENT_ADJUVANT is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_CERVICALCARCINOMAPELVICEXTENSIONTEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "6"                                                                                                                                
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NO PELVIC SPREAD PELVIC SPREAD
freq.values   "1"                       "1"              "1"          
freq.contrast "6"                       "6"              "6"          
both >= 3     "FALSE"                   "FALSE"          "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "6"                                                                         
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "6"                                                                                                                                       
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "6"                                                                      
both >= 3     "FALSE"                                                                  
Variable 41:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'LYMPH_NODES_EXAMINED':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 50:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 51:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 52:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "FEDPET_OR_CT_RESULTS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 53:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CERVIX_SUV_RESULTS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 56:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 57:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 58:'AGE_AT_DIAGNOSIS':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 59:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 194 columns, 1 survival variables, and 44 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                                  
 [2] "PATHOLOGY_T_STAGE"                               
 [3] "PATHOLOGY_N_STAGE"                               
 [4] "PATHOLOGY_M_STAGE"                               
 [5] "HISTOLOGICAL_TYPE"                               
 [6] "RADIATIONS_RADIATION_REGIMENINDICATION"          
 [7] "NUMBER_PACK_YEARS_SMOKED"                        
 [8] "NUMBER_OF_LYMPH_NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASM_HISTOLOGIC_GRADE"                       
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CHEMO_CONCURRENT_TYPE"                           
[41] "CERVIX_SUV_RESULTS"                              
[42] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[43] "AGE_AT_DIAGNOSIS"                                
[44] "STAGE_EVENT.CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=57, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
104  40   3   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  104    40     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
104  40   3   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  104    40     5 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=66, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=18, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=22, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=27, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=4, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, binary=FALSE, numeric=TRUE
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=47, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=31, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=10, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=13, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=57, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     8   3
  KRAS WILD-TYPE 142  37
  KRAS MUTATED KRAS WILD-TYPE 
            11            179 
  KRAS MUTATED KRAS WILD-TYPE 
             3             37 
$`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        50.76        12.82         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RL TCGA-FU-A3EO TCGA-FU-A57G TCGA-JW-A5VH 
        0.13        47.77         2.17         1.32         3.29 

$`KRAS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35       100.14        33.24        52.01        18.02 
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-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        58.88        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76         2.66       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        12.36 
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 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.59 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         0.92        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.35         1.97 
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       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        36.36        27.42        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58        28.37         8.28        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       30.31         7.99        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.35        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  KRAS MUTATED KRAS WILD-TYPE 
          0.13           0.03 
  KRAS MUTATED KRAS WILD-TYPE 
         57.73         210.67 
  KRAS MUTATED KRAS WILD-TYPE 
         12.82          19.86 
[1] "0.1 - 57.7 (12.8)"  "0.0 - 210.7 (19.9)"
[1] "hr=" "1.9"
D1V2, continuous
                vv
clus             T1 T2 T3+T4
  KRAS MUTATED    8  1     1
  KRAS WILD-TYPE 96 39     4
D1V3, 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"
D1V4, 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
D1V5, 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
                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                                  16
                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                                            2
D1V6, 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             16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             1              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"
D1V7, binary
                cls
clus               0   1
  KRAS MUTATED     1  10
  KRAS WILD-TYPE  31 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1   10
  KRAS WILD-TYPE   31  152
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             1             31
  YES           10            152
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, 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
D1V10, 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"
D1V11, binary
                cls
clus               0   1
  KRAS MUTATED     1   9
  KRAS WILD-TYPE  13 125
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    9
  KRAS WILD-TYPE   13  125
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            9            125
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                cls
clus              0  1
  KRAS MUTATED    4  3
  KRAS WILD-TYPE 93 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    3
  KRAS WILD-TYPE   93   28
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  TUMOR FREE            4             93
  WITH TUMOR            3             28
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  KRAS MUTATED        1      0       1             9       0
  KRAS WILD-TYPE      4     10       5           150      14
D1V14, multiclass
               clus
vv              KRAS MUTATED KRAS WILD-TYPE
  CANADA                   1              4
  RUSSIA                   0             10
  UKRAINE                  1              5
  UNITED STATES            9            150
  VIETNAM                  0             14
[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             G1 G2 G3 G4 GX
  KRAS MUTATED    1  7  3  0  0
  KRAS WILD-TYPE 13 81 79  1  8
D1V15, 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"
D1V16, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             27 
    TCGA-BI-A0VR     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1BQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DS-A3LQ     TCGA-EK-A2RA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3TX     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" 
D1V17, continuous
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  KRAS MUTATED                                             2
  KRAS WILD-TYPE                                          24
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  KRAS MUTATED                                        0
  KRAS WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  KRAS MUTATED                                                 0              2
  KRAS WILD-TYPE                                               1             35
                vv
clus             LIFELONG NON-SMOKER
  KRAS MUTATED                     4
  KRAS WILD-TYPE                  89
D1V18, multiclass
                                                 clus
vv                                                KRAS MUTATED KRAS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                2             24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             2             35
  LIFELONG NON-SMOKER                                        4             89
[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"
D1V19, continuous
D1V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  KRAS MUTATED             1        3             0        0        0
  KRAS WILD-TYPE          19       51            12        1        7
D1V21, multiclass
               clus
vv              KRAS MUTATED KRAS WILD-TYPE
  COMBINATION              1             19
  EXTERNAL                 3             51
  EXTERNAL BEAM            0             12
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D1V22, 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
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  KRAS MUTATED                    0                0                   0
  KRAS WILD-TYPE                  2                2                  20
                vv
clus             REGIONAL SITE
  KRAS MUTATED               0
  KRAS WILD-TYPE             4
D1V23, multiclass
D1V24, binary
                cls
clus              0  1
  KRAS MUTATED    0  0
  KRAS WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    0
  KRAS WILD-TYPE   16    4
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  KRAS MUTATED                                     0
  KRAS WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  KRAS MUTATED                                     0                       2
  KRAS WILD-TYPE                                   7                      26
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  KRAS MUTATED                         0                       1
  KRAS WILD-TYPE                       1                       5
D1V31, multiclass
                                     clus
vv                                    KRAS MUTATED KRAS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            0              7
  OTHER LOCATION, SPECIFY                        2             26
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              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)
  KRAS MUTATED                                               0
  KRAS WILD-TYPE                                             2
                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
D1V32, 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)                                                             2
  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"
D1V33, 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
D1V34, continuous
D1V35, continuous
D1V36, 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
D1V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  KRAS MUTATED              0           4          1
  KRAS WILD-TYPE            8          39         45
D1V38, 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"
D1V39, continuous
D1V40, 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             0         0     0
  KRAS WILD-TYPE           2        16     1
D1V41, multiclass
D1V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  KRAS MUTATED      0   0    5    3  0   0    0    0   1  0   0  1  0
  KRAS WILD-TYPE    1  21   55   19  4   7    6   10  12  1   2  1  9
D1V43, multiclass
      clus
vv     KRAS MUTATED KRAS WILD-TYPE
  T1A1            0              1
  T1B             0             21
  T1B1            5             55
  T1B2            3             19
  T2              0              4
  T2A             0              7
  T2A1            0              6
  T2A2            0             10
  T2B             1             12
  T3              0              1
  T3B             0              2
  T4              1              1
  TX              0              9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  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
D1V45, 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(2) Variable = HLA-A MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    13   2
  HLA-A WILD-TYPE 137  38
  HLA-A MUTATED HLA-A WILD-TYPE 
             15             175 
  HLA-A MUTATED HLA-A WILD-TYPE 
              2              38 
$`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       195.85        14.07 

$`HLA-A WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85         5.46        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-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        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-A7CG 
      100.14        38.43        33.24        18.02        17.85       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48        20.35        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        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        40.04        87.75        36.76         2.66       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        12.36        37.35        30.90        31.36 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       33.30        13.05        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92         6.94        14.70         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         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-A3LI TCGA-IR-A3LK 
      137.16        66.81       117.40        96.95        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-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       28.37         8.28        21.11        30.31         7.99        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        13.87 
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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  HLA-A MUTATED HLA-A WILD-TYPE 
           0.43            0.03 
  HLA-A MUTATED HLA-A WILD-TYPE 
         195.85          210.67 
  HLA-A MUTATED HLA-A WILD-TYPE 
          25.02           18.02 
[1] "0.4 - 195.8 (25.0)" "0.0 - 210.7 (18.0)"
[1] "hr=" "2.2"
D2V2, continuous
                 vv
clus              T1 T2 T3+T4
  HLA-A MUTATED    5  4     1
  HLA-A WILD-TYPE 99 36     4
D2V3, 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"
D2V4, 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
D2V5, 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
                 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                                  22
                 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                                            3
D2V6, 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              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D2V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     5  11
  HLA-A WILD-TYPE  27 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      5   11
  HLA-A WILD-TYPE   27  151
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              5              27
  YES            11             151
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, 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
D2V10, 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"
D2V11, binary
                 cls
clus                0   1
  HLA-A MUTATED     2  11
  HLA-A WILD-TYPE  12 123
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      2   11
  HLA-A WILD-TYPE   12  123
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            11             123
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                 cls
clus               0  1
  HLA-A MUTATED   13  1
  HLA-A WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     13    1
  HLA-A WILD-TYPE   84   30
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  TUMOR FREE            13              84
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  HLA-A MUTATED        0      1       0            14       1
  HLA-A WILD-TYPE      5      9       6           145      13
D2V14, multiclass
               clus
vv              HLA-A MUTATED HLA-A WILD-TYPE
  CANADA                    0               5
  RUSSIA                    1               9
  UKRAINE                   0               6
  UNITED STATES            14             145
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  HLA-A MUTATED    2  9  2  1  1
  HLA-A WILD-TYPE 12 79 80  0  7
D2V15, 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"
D2V16, continuous
D2V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  HLA-A MUTATED                                             4
  HLA-A WILD-TYPE                                          22
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  HLA-A MUTATED                                        1
  HLA-A WILD-TYPE                                      7
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  HLA-A MUTATED                                                 0
  HLA-A WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  HLA-A MUTATED                2                   8
  HLA-A WILD-TYPE             35                  85
D2V18, multiclass
                                                 clus
vv                                                HLA-A MUTATED HLA-A WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 4              22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      1               7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              2              35
  LIFELONG NON-SMOKER                                         8              85
[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"
D2V19, continuous
D2V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  HLA-A MUTATED             3        5             2        0        1
  HLA-A WILD-TYPE          17       49            10        1        6
D2V21, multiclass
               clus
vv              HLA-A MUTATED HLA-A WILD-TYPE
  COMBINATION               3              17
  EXTERNAL                  5              49
  EXTERNAL BEAM             2              10
  IMPLANTS                  0               1
  INTERNAL                  1               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"
D2V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  HLA-A MUTATED                    1                0                   4
  HLA-A WILD-TYPE                  1                2                  16
                 vv
clus              REGIONAL SITE
  HLA-A MUTATED               1
  HLA-A WILD-TYPE             3
D2V23, multiclass
                     clus
vv                    HLA-A MUTATED HLA-A WILD-TYPE
  DISTANT RECURRENCE              1               1
  LOCAL RECURRENCE                0               2
  PRIMARY TUMOR FIELD             4              16
  REGIONAL SITE                   1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
                 cls
clus               0  1
  HLA-A MUTATED    4  0
  HLA-A WILD-TYPE 12  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4    0
  HLA-A WILD-TYPE   12    4
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  CGY             4              12
  GY              0               4
[1] 2 2
[1] FALSE
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  HLA-A MUTATED                                     0
  HLA-A WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  HLA-A MUTATED                                     1                       2
  HLA-A WILD-TYPE                                   6                      26
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  HLA-A MUTATED                         0                       1
  HLA-A WILD-TYPE                       1                       5
D2V31, multiclass
                                     clus
vv                                    HLA-A MUTATED HLA-A WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             1               6
  OTHER LOCATION, SPECIFY                         2              26
  POSITIVE BLADDER MARGIN                         0               1
  POSITIVE VAGINAL MARGIN                         1               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)
  HLA-A MUTATED                                               0
  HLA-A WILD-TYPE                                             2
                 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
D2V32, 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)                                                              2
  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"
D2V33, 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
D2V34, continuous
D2V35, continuous
D2V36, 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
D2V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  HLA-A MUTATED              0           3          4
  HLA-A WILD-TYPE            8          40         42
D2V38, 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"
D2V39, continuous
D2V40, 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         3     0
  HLA-A WILD-TYPE           2        13     1
D2V41, multiclass
             clus
vv            HLA-A MUTATED HLA-A WILD-TYPE
  CARBOPLATIN             0               2
  CISPLATIN               3              13
  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"
D2V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  HLA-A MUTATED      0   2    1    2  0   0    1    1   2  1   0  0  2
  HLA-A WILD-TYPE    1  19   59   20  4   7    5    9  11  0   2  2  7
D2V43, multiclass
      clus
vv     HLA-A MUTATED HLA-A WILD-TYPE
  T1A1             0               1
  T1B              2              19
  T1B1             1              59
  T1B2             2              20
  T2               0               4
  T2A              0               7
  T2A1             1               5
  T2A2             1               9
  T2B              2              11
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               2               7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  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
D2V45, 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(3) Variable = FBXW7 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    15   4
  FBXW7 WILD-TYPE 135  36
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             171 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              36 
$`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        50.76       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         0.59        47.77 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A2QG TCGA-FU-A57G TCGA-FU-A5XV TCGA-JW-A5VJ 
        0.10         0.03         0.92         1.32         1.97        21.44 
TCGA-Q1-A73O 
       14.07 

$`FBXW7 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        30.21        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-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       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-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        58.88        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HT 
       17.52         8.28        39.55        12.36        30.90        31.36 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       33.30        13.05        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       26.01        12.66        12.82        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM 
       45.96        26.27         6.64         1.51        19.27         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36         1.18         2.24         0.10         0.07         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A770 
        1.58         1.48         0.82         3.52         1.35         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       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       29.85        36.36        27.42         3.29        24.56        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       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        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        13.87        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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.03            0.03 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         210.67          195.85 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          21.44           19.59 
[1] "0.0 - 210.7 (21.4)" "0.0 - 195.8 (19.6)"
[1] "hr=" "1.1"
D3V2, continuous
                 vv
clus              T1 T2 T3+T4
  FBXW7 MUTATED   11  2     2
  FBXW7 WILD-TYPE 93 38     3
D3V3, 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"
D3V4, 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
D3V5, 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
                 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                                  18
                 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                                            3
D3V6, 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              18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D3V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     4  15
  FBXW7 WILD-TYPE  28 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      4   15
  FBXW7 WILD-TYPE   28  147
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              4              28
  YES            15             147
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, 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
D3V10, 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"
D3V11, binary
                 cls
clus                0   1
  FBXW7 MUTATED     2  14
  FBXW7 WILD-TYPE  12 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2   14
  FBXW7 WILD-TYPE   12  120
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            14             120
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                 cls
clus               0  1
  FBXW7 MUTATED    7  5
  FBXW7 WILD-TYPE 90 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      7    5
  FBXW7 WILD-TYPE   90   26
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  TUMOR FREE             7              90
  WITH TUMOR             5              26
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  FBXW7 MUTATED        1      2       0            15       1
  FBXW7 WILD-TYPE      4      8       6           144      13
D3V14, multiclass
               clus
vv              FBXW7 MUTATED FBXW7 WILD-TYPE
  CANADA                    1               4
  RUSSIA                    2               8
  UKRAINE                   0               6
  UNITED STATES            15             144
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  FBXW7 MUTATED    0  9  8  0  1
  FBXW7 WILD-TYPE 14 79 74  1  7
D3V15, 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"
D3V16, continuous
D3V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  FBXW7 MUTATED                                             3
  FBXW7 WILD-TYPE                                          23
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  FBXW7 MUTATED                                        0
  FBXW7 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  FBXW7 MUTATED                                                 0
  FBXW7 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  FBXW7 MUTATED                1                  10
  FBXW7 WILD-TYPE             36                  83
D3V18, multiclass
                                                 clus
vv                                                FBXW7 MUTATED FBXW7 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 3              23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                        10              83
[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"
D3V19, continuous
D3V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  FBXW7 MUTATED             1        2             2        1        0
  FBXW7 WILD-TYPE          19       52            10        0        7
D3V21, multiclass
               clus
vv              FBXW7 MUTATED FBXW7 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  2              52
  EXTERNAL BEAM             2              10
  IMPLANTS                  1               0
  INTERNAL                  0               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"
D3V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  FBXW7 MUTATED                    0                0                   0
  FBXW7 WILD-TYPE                  2                2                  20
                 vv
clus              REGIONAL SITE
  FBXW7 MUTATED               0
  FBXW7 WILD-TYPE             4
D3V23, multiclass
D3V24, binary
                 cls
clus               0  1
  FBXW7 MUTATED    0  0
  FBXW7 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0    0
  FBXW7 WILD-TYPE   16    4
D3V25, continuous
D3V26, continuous
D3V27, continuous
D3V28, continuous
D3V29, continuous
D3V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FBXW7 MUTATED                                     0
  FBXW7 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FBXW7 MUTATED                                     0                       4
  FBXW7 WILD-TYPE                                   7                      24
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FBXW7 MUTATED                         1                       0
  FBXW7 WILD-TYPE                       0                       6
D3V31, multiclass
                                     clus
vv                                    FBXW7 MUTATED FBXW7 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             0               7
  OTHER LOCATION, SPECIFY                         4              24
  POSITIVE BLADDER MARGIN                         1               0
  POSITIVE VAGINAL MARGIN                         0               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)
  FBXW7 MUTATED                                               0
  FBXW7 WILD-TYPE                                             2
                 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
D3V32, 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)                                                              2
  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"
D3V33, 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
D3V34, continuous
D3V35, continuous
D3V36, 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
D3V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  FBXW7 MUTATED              2           5          5
  FBXW7 WILD-TYPE            6          38         41
D3V38, 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"
D3V39, continuous
D3V40, 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         1     0
  FBXW7 WILD-TYPE           1        15     1
D3V41, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2              17 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1MH 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A3LQ      TCGA-EK-A2H0      TCGA-EK-A2H1 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-HM-A3JJ 
"FBXW7 WILD-TYPE" 
D3V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  FBXW7 MUTATED      0   2    6    3  0   1    0    0   1  0   1  1  2
  FBXW7 WILD-TYPE    1  19   54   19  4   6    6   10  12  1   1  1  7
D3V43, multiclass
      clus
vv     FBXW7 MUTATED FBXW7 WILD-TYPE
  T1A1             0               1
  T1B              2              19
  T1B1             6              54
  T1B2             3              19
  T2               0               4
  T2A              1               6
  T2A1             0               6
  T2A2             0              10
  T2B              1              12
  T3               0               1
  T3B              1               1
  T4               1               1
  TX               2               7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V44, 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
D3V45, 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(4) Variable = HLA-B MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     9   2
  HLA-B WILD-TYPE 141  38
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             179 
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              38 
$`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         1.58        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       195.85        15.95        14.07 

$`HLA-B WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46         2.43        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        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.45         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        96.95 
TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       81.96        27.42         3.29        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        30.31         7.99        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        13.87        34.62 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       54.81        35.05        20.84        15.58        16.41         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        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  HLA-B MUTATED HLA-B WILD-TYPE 
           1.58            0.03 
  HLA-B MUTATED HLA-B WILD-TYPE 
         195.85          210.67 
  HLA-B MUTATED HLA-B WILD-TYPE 
          24.56           19.36 
[1] "1.6 - 195.8 (24.6)" "0.0 - 210.7 (19.4)"
[1] "hr=" "1.6"
D4V2, continuous
                 vv
clus               T1  T2 T3+T4
  HLA-B MUTATED     3   3     1
  HLA-B WILD-TYPE 101  37     4
D4V3, 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"
D4V4, 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
D4V5, 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
                 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                                  22
                 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                                            3
D4V6, 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              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D4V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     2   9
  HLA-B WILD-TYPE  30 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    9
  HLA-B WILD-TYPE   30  153
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              2              30
  YES             9             153
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, 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
D4V10, 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"
D4V11, binary
                 cls
clus                0   1
  HLA-B MUTATED     3   3
  HLA-B WILD-TYPE  11 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    3
  HLA-B WILD-TYPE   11  131
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 3              11
  NOT HISPANIC OR LATINO             3             131
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                 cls
clus               0  1
  HLA-B MUTATED    7  3
  HLA-B WILD-TYPE 90 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      7    3
  HLA-B WILD-TYPE   90   28
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  TUMOR FREE             7              90
  WITH TUMOR             3              28
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  HLA-B MUTATED        0      0       0            11       0
  HLA-B WILD-TYPE      5     10       6           148      14
D4V14, multiclass
               clus
vv              HLA-B MUTATED HLA-B WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES            11             148
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  HLA-B MUTATED    1  5  3  1  1
  HLA-B WILD-TYPE 13 83 79  0  7
D4V15, 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"
D4V16, continuous
D4V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  HLA-B MUTATED                                             3
  HLA-B WILD-TYPE                                          23
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  HLA-B MUTATED                                        0
  HLA-B WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  HLA-B MUTATED                                                 0
  HLA-B WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  HLA-B MUTATED                3                   5
  HLA-B WILD-TYPE             34                  88
D4V18, multiclass
                                                 clus
vv                                                HLA-B MUTATED HLA-B WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 3              23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              3              34
  LIFELONG NON-SMOKER                                         5              88
[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"
D4V19, continuous
D4V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  HLA-B MUTATED             2        7             0        0        0
  HLA-B WILD-TYPE          18       47            12        1        7
D4V21, multiclass
               clus
vv              HLA-B MUTATED HLA-B WILD-TYPE
  COMBINATION               2              18
  EXTERNAL                  7              47
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D4V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  HLA-B MUTATED                    0                0                   2
  HLA-B WILD-TYPE                  2                2                  18
                 vv
clus              REGIONAL SITE
  HLA-B MUTATED               0
  HLA-B WILD-TYPE             4
D4V23, multiclass
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              26 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LF      TCGA-JW-A5VG      TCGA-JX-A5QV 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-R2-A69V      TCGA-WL-A834 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
D4V24, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  0
  HLA-B WILD-TYPE 14  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    0
  HLA-B WILD-TYPE   14    4
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  CGY             2              14
  GY              0               4
[1] 2 2
[1] FALSE
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  HLA-B MUTATED                                     0
  HLA-B WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  HLA-B MUTATED                                     1                       0
  HLA-B WILD-TYPE                                   6                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  HLA-B MUTATED                         0                       1
  HLA-B WILD-TYPE                       1                       5
D4V31, multiclass
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-EX-A449      TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LI 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  HLA-B MUTATED                                               0
  HLA-B WILD-TYPE                                             2
                 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
D4V32, 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)                                                              2
  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"
D4V33, 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
D4V34, continuous
D4V35, continuous
D4V36, 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
D4V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  HLA-B MUTATED              0           3          2
  HLA-B WILD-TYPE            8          40         44
D4V38, 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"
D4V39, continuous
D4V40, 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         0     0
  HLA-B WILD-TYPE           2        16     1
D4V41, multiclass
D4V42, 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" 
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  HLA-B MUTATED      0   0    1    2  0   0    1    0   2  1   0  0  2
  HLA-B WILD-TYPE    1  21   59   20  4   7    5   10  11  0   2  2  7
D4V43, multiclass
      clus
vv     HLA-B MUTATED HLA-B WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             1              59
  T1B2             2              20
  T2               0               4
  T2A              0               7
  T2A1             1               5
  T2A2             0              10
  T2B              2              11
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               2               7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V44, 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
D4V45, 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(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    10   4
  PTEN WILD-TYPE 140  36
  PTEN MUTATED PTEN WILD-TYPE 
            14            176 
  PTEN MUTATED PTEN WILD-TYPE 
             4             36 
$`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        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2PM TCGA-FU-A23K TCGA-FU-A3HZ TCGA-FU-A3TQ 
       14.89        26.79         0.59         1.22        36.26         1.58 
TCGA-JW-A5VH TCGA-Q1-A6DW 
        3.29        17.56 

$`PTEN WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       57.04        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      144.16       177.04       173.29         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-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       154.32       101.82       134.33        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        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ 
        2.66       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        12.36        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        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E 
       26.40        24.56        14.50        26.01        12.66         7.46 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L 
        7.92         6.94        14.70        19.79         8.32        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17        31.36         1.45         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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       117.40        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        21.11       195.85        30.31         7.99 
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 
       13.87        34.62        54.81        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        15.39        19.36        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  PTEN MUTATED PTEN WILD-TYPE 
          0.59           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         82.85         210.67 
  PTEN MUTATED PTEN WILD-TYPE 
         16.52          20.07 
[1] "0.6 - 82.8 (16.5)"  "0.0 - 210.7 (20.1)"
[1] "hr=" "2.1"
D5V2, continuous
                vv
clus             T1 T2 T3+T4
  PTEN MUTATED    6  4     1
  PTEN WILD-TYPE 98 36     4
D5V3, 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"
D5V4, 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
D5V5, 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
                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                                  21
                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                                            3
D5V6, 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             21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D5V7, binary
                cls
clus               0   1
  PTEN MUTATED     2  13
  PTEN WILD-TYPE  30 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   13
  PTEN WILD-TYPE   30  149
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             2             30
  YES           13            149
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, 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
D5V10, 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"
D5V11, binary
                cls
clus               0   1
  PTEN MUTATED     1  10
  PTEN WILD-TYPE  13 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   10
  PTEN WILD-TYPE   13  124
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO           10            124
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                cls
clus              0  1
  PTEN MUTATED    7  1
  PTEN WILD-TYPE 90 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      7    1
  PTEN WILD-TYPE   90   30
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  TUMOR FREE            7             90
  WITH TUMOR            1             30
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  PTEN MUTATED        0      1       2            12       0
  PTEN WILD-TYPE      5      9       4           147      14
D5V14, multiclass
               clus
vv              PTEN MUTATED PTEN WILD-TYPE
  CANADA                   0              5
  RUSSIA                   1              9
  UKRAINE                  2              4
  UNITED STATES           12            147
  VIETNAM                  0             14
[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             G1 G2 G3 G4 GX
  PTEN MUTATED    0  8  6  0  1
  PTEN WILD-TYPE 14 80 76  1  7
D5V15, 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"
D5V16, continuous
D5V17, continuous
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  PTEN MUTATED                                             4
  PTEN WILD-TYPE                                          22
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  PTEN MUTATED                                        0
  PTEN WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  PTEN MUTATED                                                 0              3
  PTEN WILD-TYPE                                               1             34
                vv
clus             LIFELONG NON-SMOKER
  PTEN MUTATED                     6
  PTEN WILD-TYPE                  87
D5V18, multiclass
                                                 clus
vv                                                PTEN MUTATED PTEN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                4             22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             3             34
  LIFELONG NON-SMOKER                                        6             87
[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"
D5V19, continuous
D5V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  PTEN MUTATED             1        4             1        0        3
  PTEN WILD-TYPE          19       50            11        1        4
D5V21, multiclass
               clus
vv              PTEN MUTATED PTEN WILD-TYPE
  COMBINATION              1             19
  EXTERNAL                 4             50
  EXTERNAL BEAM            1             11
  IMPLANTS                 0              1
  INTERNAL                 3              4
[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"
D5V22, 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
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  PTEN MUTATED                    0                0                   2
  PTEN WILD-TYPE                  2                2                  18
                vv
clus             REGIONAL SITE
  PTEN MUTATED               2
  PTEN WILD-TYPE             2
D5V23, multiclass
                     clus
vv                    PTEN MUTATED PTEN WILD-TYPE
  DISTANT RECURRENCE             0              2
  LOCAL RECURRENCE               0              2
  PRIMARY TUMOR FIELD            2             18
  REGIONAL SITE                  2              2
[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"
D5V24, binary
                cls
clus              0  1
  PTEN MUTATED    1  2
  PTEN WILD-TYPE 15  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    2
  PTEN WILD-TYPE   15    2
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  CGY            1             15
  GY             2              2
[1] 2 2
[1] FALSE
D5V25, continuous
D5V26, continuous
D5V27, continuous
D5V28, continuous
D5V29, continuous
D5V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  PTEN MUTATED                                     0
  PTEN WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  PTEN MUTATED                                     0                       1
  PTEN WILD-TYPE                                   7                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  PTEN MUTATED                         0                       1
  PTEN WILD-TYPE                       1                       5
D5V31, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2             42 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BK 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MJ     TCGA-C5-A1MP 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2M1     TCGA-C5-A3HE     TCGA-C5-A7CG 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-DG-A2KL     TCGA-DR-A0ZM 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EA-A50E     TCGA-EK-A2RN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-EX-A1H5     TCGA-EX-A449     TCGA-FU-A3EO 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  PTEN MUTATED                                               0
  PTEN WILD-TYPE                                             2
                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
D5V32, 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)                                                             2
  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"
D5V33, 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
D5V34, continuous
D5V35, continuous
D5V36, 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
D5V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  PTEN MUTATED              0           0          3
  PTEN WILD-TYPE            8          43         43
D5V38, 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"
D5V39, continuous
D5V40, 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             0         0     0
  PTEN WILD-TYPE           2        16     1
D5V41, multiclass
D5V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  PTEN MUTATED      0   0    4    2  1   0    0    1   2  0   0  1  1
  PTEN WILD-TYPE    1  21   56   20  3   7    6    9  11  1   2  1  8
D5V43, multiclass
      clus
vv     PTEN MUTATED PTEN WILD-TYPE
  T1A1            0              1
  T1B             0             21
  T1B1            4             56
  T1B2            2             20
  T2              1              3
  T2A             0              7
  T2A1            0              6
  T2A2            1              9
  T2B             2             11
  T3              0              1
  T3B             0              2
  T4              1              1
  TX              1              8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V44, 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
D5V45, 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(6) Variable = ARID1A MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     9   4
  ARID1A WILD-TYPE 141  36
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              177 
  ARID1A MUTATED ARID1A WILD-TYPE 
               4               36 
$`ARID1A MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MK TCGA-DS-A7WH TCGA-EA-A4BA TCGA-EX-A449 
       35.01        35.61         2.43        17.52        12.82        14.70 
TCGA-FU-A3HZ TCGA-FU-A57G TCGA-IR-A3LA TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JX-A3Q0 
       36.26         1.32       137.16         3.29        15.58       195.85 
TCGA-Q1-A73O 
       14.07 

$`ARID1A WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99         0.46        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        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       58.88        36.76         2.66       117.99       118.65        28.90 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       22.98        16.83        16.18         8.28        39.55        12.36 
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 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        47.77         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.35         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        29.85        36.36        27.42        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        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        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        13.87        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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  ARID1A MUTATED ARID1A WILD-TYPE 
            1.32             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
          195.85           210.67 
  ARID1A MUTATED ARID1A WILD-TYPE 
           15.58            19.86 
[1] "1.3 - 195.8 (15.6)" "0.0 - 210.7 (19.9)"
[1] "hr=" "1.4"
D6V2, continuous
                  vv
clus               T1 T2 T3+T4
  ARID1A MUTATED    7  1     3
  ARID1A WILD-TYPE 97 39     2
D6V3, 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"
D6V4, 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
D6V5, 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
                  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                                     6
  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                                              0
  ARID1A WILD-TYPE                                            3
D6V6, 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                        6               16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  1                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D6V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     3  11
  ARID1A WILD-TYPE  29 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3   11
  ARID1A WILD-TYPE   29  151
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               3               29
  YES             11              151
[1] 2 2
[1] FALSE
D6V8, 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" 
D6V9, 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
D6V10, 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"
D6V11, binary
                  cls
clus                 0   1
  ARID1A MUTATED     4   9
  ARID1A WILD-TYPE  10 125
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    9
  ARID1A WILD-TYPE   10  125
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  4               10
  NOT HISPANIC OR LATINO              9              125
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                  cls
clus                0  1
  ARID1A MUTATED    8  4
  ARID1A WILD-TYPE 89 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8    4
  ARID1A WILD-TYPE   89   27
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  TUMOR FREE              8               89
  WITH TUMOR              4               27
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  ARID1A MUTATED        0      0       1            13       0
  ARID1A WILD-TYPE      5     10       5           146      14
D6V14, multiclass
               clus
vv              ARID1A MUTATED ARID1A WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    1                5
  UNITED STATES             13              146
  VIETNAM                    0               14
[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               G1 G2 G3 G4 GX
  ARID1A MUTATED    2  7  4  0  1
  ARID1A WILD-TYPE 12 81 78  1  7
D6V15, 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"
D6V16, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               28 
      TCGA-BI-A0VR       TCGA-C5-A1BJ       TCGA-C5-A1BL       TCGA-C5-A1BQ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A2M2 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-DG-A2KK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-EK-A2RA       TCGA-EX-A69M       TCGA-FU-A2QG 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A3TX       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" 
D6V17, 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" 
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  ARID1A MUTATED                                             1
  ARID1A WILD-TYPE                                          25
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  ARID1A MUTATED                                        0
  ARID1A WILD-TYPE                                      8
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  ARID1A MUTATED                                                 0
  ARID1A WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  ARID1A MUTATED                1                  11
  ARID1A WILD-TYPE             36                  82
D6V18, multiclass
                                                 clus
vv                                                ARID1A MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               1
  LIFELONG NON-SMOKER                                         11
                                                 clus
vv                                                ARID1A WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                36
  LIFELONG NON-SMOKER                                           82
[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"
D6V19, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               50 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ       TCGA-C5-A1BL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A1MF       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-A7CL       TCGA-C5-A7CO 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DR-A0ZM       TCGA-DS-A5RQ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EA-A556       TCGA-EK-A2RA       TCGA-EX-A1H5       TCGA-FU-A2QG 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ       TCGA-FU-A3TX 
"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" 
D6V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  ARID1A MUTATED             2        8             1        0        0
  ARID1A WILD-TYPE          18       46            11        1        7
D6V21, multiclass
               clus
vv              ARID1A MUTATED ARID1A WILD-TYPE
  COMBINATION                2               18
  EXTERNAL                   8               46
  EXTERNAL BEAM              1               11
  IMPLANTS                   0                1
  INTERNAL                   0                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"
D6V22, 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
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  ARID1A MUTATED                    0                0                   2
  ARID1A WILD-TYPE                  2                2                  18
                  vv
clus               REGIONAL SITE
  ARID1A MUTATED               0
  ARID1A WILD-TYPE             4
D6V23, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               26 
      TCGA-C5-A0TN       TCGA-C5-A1BF       TCGA-C5-A1BQ       TCGA-C5-A2LZ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7CO 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-C5-A7UH       TCGA-C5-A7X3       TCGA-DG-A2KL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DS-A7WF       TCGA-EA-A43B       TCGA-EA-A5FO       TCGA-EX-A3L1 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FU-A23L       TCGA-FU-A3HY       TCGA-HM-A3JJ       TCGA-HM-A4S6 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-JW-A5VG       TCGA-JX-A5QV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-R2-A69V       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D6V24, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  0
  ARID1A WILD-TYPE 14  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    0
  ARID1A WILD-TYPE   14    4
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  CGY              2               14
  GY               0                4
[1] 2 2
[1] FALSE
D6V25, continuous
D6V26, continuous
D6V27, continuous
D6V28, continuous
D6V29, continuous
D6V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ARID1A MUTATED                                     1
  ARID1A WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ARID1A MUTATED                                     0                       1
  ARID1A WILD-TYPE                                   7                      27
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ARID1A MUTATED                         0                       0
  ARID1A WILD-TYPE                       1                       6
D6V31, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               42 
      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-A2KL 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DR-A0ZM       TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EA-A50E 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EK-A2RN       TCGA-EK-A2RO       TCGA-EX-A1H5       TCGA-FU-A3EO 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LK 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             2
                  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
D6V32, 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)                                                               2
  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"
D6V33, 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
D6V34, continuous
D6V35, continuous
D6V36, 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
D6V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  ARID1A MUTATED              0           3          3
  ARID1A WILD-TYPE            8          40         43
D6V38, 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"
D6V39, continuous
D6V40, 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             1         2     0
  ARID1A WILD-TYPE           1        14     1
D6V41, multiclass
             clus
vv            ARID1A MUTATED ARID1A WILD-TYPE
  CARBOPLATIN              1                1
  CISPLATIN                2               14
  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"
D6V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  ARID1A MUTATED      0   0    4    3  0   0    0    1   0  1   1  1  1
  ARID1A WILD-TYPE    1  21   56   19  4   7    6    9  13  0   1  1  8
D6V43, multiclass
      clus
vv     ARID1A MUTATED ARID1A WILD-TYPE
  T1A1              0                1
  T1B               0               21
  T1B1              4               56
  T1B2              3               19
  T2                0                4
  T2A               0                7
  T2A1              0                6
  T2A2              1                9
  T2B               0               13
  T3                1                0
  T3B               1                1
  T4                1                1
  TX                1                8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V44, 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
D6V45, 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(7) Variable = MAPK1 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  MAPK1 MUTATED     9   0
  MAPK1 WILD-TYPE 141  40
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             181 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              0              40 
$`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        15.02 
TCGA-EK-A2RA TCGA-FU-A3TQ TCGA-HM-A3JK 
       16.08         1.58        20.78 

$`MAPK1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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-A2KM 
      131.11         9.34         1.12        58.88        50.76        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1OA 
       87.75        58.88        36.76         2.66       117.99        28.90 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
       22.98        16.83        16.18        17.52         8.28        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       37.35        30.90        33.30        13.05        25.02        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        14.50        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF 
        7.46        14.89        26.79        13.91        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.13         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26         1.45         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        21.67        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       117.40        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-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       195.85        30.31         7.99        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        13.87        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  MAPK1 MUTATED MAPK1 WILD-TYPE 
           1.58            0.03 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
         118.65          210.67 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
          31.36           19.36 
[1] "1.6 - 118.7 (31.4)" "0.0 - 210.7 (19.4)"
[1] "hr="     "2.7e+07"
D7V2, continuous
                 vv
clus               T1  T2 T3+T4
  MAPK1 MUTATED     4   4     0
  MAPK1 WILD-TYPE 100  36     5
D7V3, 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"
D7V4, 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
D7V5, 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
                 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                                  22
                 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                                            3
D7V6, 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              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D7V7, binary
                 cls
clus                0   1
  MAPK1 MUTATED     3   6
  MAPK1 WILD-TYPE  29 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    6
  MAPK1 WILD-TYPE   29  156
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  NO              3              29
  YES             6             156
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, 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
D7V10, 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"
D7V11, binary
                 cls
clus                0   1
  MAPK1 MUTATED     1   7
  MAPK1 WILD-TYPE  13 127
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      1    7
  MAPK1 WILD-TYPE   13  127
                        clus
vv                       MAPK1 MUTATED MAPK1 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             7             127
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                 cls
clus               0  1
  MAPK1 MUTATED    6  1
  MAPK1 WILD-TYPE 91 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      6    1
  MAPK1 WILD-TYPE   91   30
            clus
vv           MAPK1 MUTATED MAPK1 WILD-TYPE
  TUMOR FREE             6              91
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  MAPK1 MUTATED        1      2       0             5       1
  MAPK1 WILD-TYPE      4      8       6           154      13
D7V14, multiclass
               clus
vv              MAPK1 MUTATED MAPK1 WILD-TYPE
  CANADA                    1               4
  RUSSIA                    2               8
  UKRAINE                   0               6
  UNITED STATES             5             154
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  MAPK1 MUTATED    2  5  2  0  0
  MAPK1 WILD-TYPE 12 83 80  1  8
D7V15, 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"
D7V16, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2              27 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BQ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX 
"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" 
D7V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  MAPK1 MUTATED                                             2
  MAPK1 WILD-TYPE                                          24
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  MAPK1 MUTATED                                        0
  MAPK1 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  MAPK1 MUTATED                                                 0
  MAPK1 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  MAPK1 MUTATED                3                   4
  MAPK1 WILD-TYPE             34                  89
D7V18, multiclass
                                                 clus
vv                                                MAPK1 MUTATED MAPK1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 2              24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              3              34
  LIFELONG NON-SMOKER                                         4              89
[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"
D7V19, continuous
D7V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  MAPK1 MUTATED             1        1             2        0        0
  MAPK1 WILD-TYPE          19       53            10        1        7
D7V21, multiclass
               clus
vv              MAPK1 MUTATED MAPK1 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  1              53
  EXTERNAL BEAM             2              10
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D7V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  MAPK1 MUTATED                    0                0                   1
  MAPK1 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  MAPK1 MUTATED               0
  MAPK1 WILD-TYPE             4
D7V23, multiclass
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DS-A7WF 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1      TCGA-FU-A23L 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D7V24, binary
                 cls
clus               0  1
  MAPK1 MUTATED    1  0
  MAPK1 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      1    0
  MAPK1 WILD-TYPE   15    4
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D7V25, continuous
D7V26, continuous
D7V27, continuous
D7V28, continuous
D7V29, continuous
D7V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MAPK1 MUTATED                                     0
  MAPK1 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MAPK1 MUTATED                                     0                       1
  MAPK1 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MAPK1 MUTATED                         0                       1
  MAPK1 WILD-TYPE                       1                       5
D7V31, multiclass
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E      TCGA-EK-A2RN 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449      TCGA-FU-A3EO 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  MAPK1 MUTATED                                               0
  MAPK1 WILD-TYPE                                             2
                 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
D7V32, 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)                                                              2
  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"
D7V33, 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
D7V34, continuous
D7V35, continuous
D7V36, 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
D7V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  MAPK1 MUTATED              0           2          3
  MAPK1 WILD-TYPE            8          41         43
D7V38, 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"
D7V39, continuous
D7V40, 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         1     0
  MAPK1 WILD-TYPE           2        15     1
D7V41, multiclass
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BN      TCGA-C5-A1M9      TCGA-C5-A1MH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D7V42, 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" 
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  MAPK1 MUTATED      0   1    2    1  0   1    0    1   2  0   0  0  0
  MAPK1 WILD-TYPE    1  20   58   21  4   6    6    9  11  1   2  2  9
D7V43, multiclass
      clus
vv     MAPK1 MUTATED MAPK1 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             2              58
  T1B2             1              21
  T2               0               4
  T2A              1               6
  T2A1             0               6
  T2A2             1               9
  T2B              2              11
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V44, 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
D7V45, 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(8) Variable = EP300 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    17   3
  EP300 WILD-TYPE 133  37
  EP300 MUTATED EP300 WILD-TYPE 
             20             170 
  EP300 MUTATED EP300 WILD-TYPE 
              3              37 
$`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-A3GK TCGA-EX-A1H5 TCGA-FU-A3HY 
       13.91         0.59         1.45         0.10        20.35        31.36 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-IR-A3LK TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-LP-A5U2 
        1.45         1.58        29.85         8.28       195.85         0.30 
TCGA-MY-A5BD TCGA-MY-A5BE 
       54.81        35.05 

$`EP300 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        53.16        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 
       15.48        20.35       147.35        17.19       155.77         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       58.88        36.76         2.66       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-A3HR TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       12.36        30.90        31.36        25.02        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        14.50        26.01        12.66        12.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       14.89        26.79        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
       19.27         0.43         0.59         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.07         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         8.32         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        2.17        36.26         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         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       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ 
       24.56        21.44        20.48        15.58        28.37        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       30.31         7.99        11.28         0.89        12.49         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       13.35        13.87        34.62        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        15.39        19.36        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  EP300 MUTATED EP300 WILD-TYPE 
           0.10            0.03 
  EP300 MUTATED EP300 WILD-TYPE 
         210.67          177.04 
  EP300 MUTATED EP300 WILD-TYPE 
         25.100          19.475 
[1] "0.1 - 210.7 (25.1)" "0.0 - 177.0 (19.5)"
[1] "hr=" "1.6"
D8V2, continuous
                 vv
clus              T1 T2 T3+T4
  EP300 MUTATED   10  7     1
  EP300 WILD-TYPE 94 33     4
D8V3, 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"
D8V4, 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
D8V5, 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
                 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                                  21
                 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                                            3
D8V6, 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              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D8V7, binary
                 cls
clus                0   1
  EP300 MUTATED     2  19
  EP300 WILD-TYPE  30 143
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   19
  EP300 WILD-TYPE   30  143
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              2              30
  YES            19             143
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, 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
D8V10, 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"
D8V11, binary
                 cls
clus                0   1
  EP300 MUTATED     2  17
  EP300 WILD-TYPE  12 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   17
  EP300 WILD-TYPE   12  117
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            17             117
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                 cls
clus               0  1
  EP300 MUTATED   11  3
  EP300 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     11    3
  EP300 WILD-TYPE   86   28
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  TUMOR FREE            11              86
  WITH TUMOR             3              28
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  EP300 MUTATED        0      2       1            17       1
  EP300 WILD-TYPE      5      8       5           142      13
D8V14, multiclass
               clus
vv              EP300 MUTATED EP300 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    2               8
  UKRAINE                   1               5
  UNITED STATES            17             142
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  EP300 MUTATED    1  9 11  0  0
  EP300 WILD-TYPE 13 79 71  1  8
D8V15, 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"
D8V16, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              27 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BQ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A2M2      TCGA-C5-A3HD 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-DS-A3LQ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX 
"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" 
D8V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  EP300 MUTATED                                             1
  EP300 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  EP300 MUTATED                                        1
  EP300 WILD-TYPE                                      7
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  EP300 MUTATED                                                 0
  EP300 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  EP300 MUTATED                4                  11
  EP300 WILD-TYPE             33                  82
D8V18, multiclass
                                                 clus
vv                                                EP300 MUTATED EP300 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      1               7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              4              33
  LIFELONG NON-SMOKER                                        11              82
[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"
D8V19, continuous
D8V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  EP300 MUTATED             1        6             0        0        1
  EP300 WILD-TYPE          19       48            12        1        6
D8V21, multiclass
               clus
vv              EP300 MUTATED EP300 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  6              48
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  1               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"
D8V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  EP300 MUTATED                    0                0                   2
  EP300 WILD-TYPE                  2                2                  18
                 vv
clus              REGIONAL SITE
  EP300 MUTATED               1
  EP300 WILD-TYPE             3
D8V23, multiclass
                     clus
vv                    EP300 MUTATED EP300 WILD-TYPE
  DISTANT RECURRENCE              0               2
  LOCAL RECURRENCE                0               2
  PRIMARY TUMOR FIELD             2              18
  REGIONAL SITE                   1               3
[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"
D8V24, binary
                 cls
clus               0  1
  EP300 MUTATED    2  0
  EP300 WILD-TYPE 14  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2    0
  EP300 WILD-TYPE   14    4
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  CGY             2              14
  GY              0               4
[1] 2 2
[1] FALSE
D8V25, continuous
D8V26, continuous
D8V27, continuous
D8V28, continuous
D8V29, continuous
D8V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  EP300 MUTATED                                     0
  EP300 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  EP300 MUTATED                                     2                       1
  EP300 WILD-TYPE                                   5                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  EP300 MUTATED                         0                       0
  EP300 WILD-TYPE                       1                       6
D8V31, multiclass
                                     clus
vv                                    EP300 MUTATED EP300 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             2               5
  OTHER LOCATION, SPECIFY                         1              27
  POSITIVE BLADDER MARGIN                         0               1
  POSITIVE VAGINAL MARGIN                         0               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)
  EP300 MUTATED                                               0
  EP300 WILD-TYPE                                             2
                 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
D8V32, 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)                                                              2
  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"
D8V33, 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
D8V34, continuous
D8V35, continuous
D8V36, 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
D8V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  EP300 MUTATED              1           3          8
  EP300 WILD-TYPE            7          40         38
D8V38, 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"
D8V39, continuous
D8V40, 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         1     0
  EP300 WILD-TYPE           2        15     1
D8V41, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 
D8V42, 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" 
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  EP300 MUTATED      0   1    5    4  0   2    0    1   4  1   0  0  0
  EP300 WILD-TYPE    1  20   55   18  4   5    6    9   9  0   2  2  9
D8V43, multiclass
      clus
vv     EP300 MUTATED EP300 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             5              55
  T1B2             4              18
  T2               0               4
  T2A              2               5
  T2A1             0               6
  T2A2             1               9
  T2B              4               9
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V44, 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
D8V45, 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(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    38  13
  PIK3CA WILD-TYPE 112  27
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              51              139 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              13               27 
$`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 
       50.76        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 
       12.82         7.46        26.79         1.51         0.59         0.03 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-FU-A23K TCGA-FU-A3HY TCGA-FU-A3HZ 
        0.10         0.07         0.10         1.22        31.36        36.26 
TCGA-FU-A3WB TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        0.82         1.32        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 
      195.85        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-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        18.74        36.56 
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-A1MI TCGA-C5-A1MJ 
       30.21        35.01        57.73        53.16        35.61         0.46 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       83.05        78.35       100.14        33.24        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       154.32       134.33        15.48        20.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KM 
       17.19       155.77         9.34         1.12        58.88        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       28.90        22.98        17.52         8.28        39.55        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       37.35        30.90        33.30        13.05        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 
       24.56        14.50        26.01        12.66        14.89        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 
       45.96        26.27         6.64        19.27         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        1.45         0.13        16.08         0.07         4.04         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        1.18        47.77         2.24         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L 
        7.92         6.94        14.70        19.79         8.32        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ 
        0.92         2.17         1.45         1.58         1.48         3.52 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.35         1.97         1.12        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LL 
        9.44       147.39       137.16        66.81       117.40        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV 
       27.42        24.56        20.48        21.11        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
       11.28         0.89        12.49         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O 
       34.62        20.84        16.41         9.04        17.56        14.07 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        9.34        15.39        19.36         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.03             0.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          195.85           210.67 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           20.91            19.27 
[1] "0.0 - 195.8 (20.9)" "0.0 - 210.7 (19.3)"
[1] "hr=" "1.2"
D9V2, continuous
                  vv
clus               T1 T2 T3+T4
  PIK3CA MUTATED   26 12     3
  PIK3CA WILD-TYPE 78 28     2
D9V3, 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"
D9V4, 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
D9V5, 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
                  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                                  14
                  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                                            1
D9V6, 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               14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               2                1
[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"
D9V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     6  47
  PIK3CA WILD-TYPE  26 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      6   47
  PIK3CA WILD-TYPE   26  115
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               6               26
  YES             47              115
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, 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
D9V10, 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"
D9V11, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     9  29
  PIK3CA WILD-TYPE   5 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      9   29
  PIK3CA WILD-TYPE    5  105
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  9                5
  NOT HISPANIC OR LATINO             29              105
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                  cls
clus                0  1
  PIK3CA MUTATED   27 11
  PIK3CA WILD-TYPE 70 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     27   11
  PIK3CA WILD-TYPE   70   20
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  TUMOR FREE             27               70
  WITH TUMOR             11               20
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  PIK3CA MUTATED        2      2       2            44       3
  PIK3CA WILD-TYPE      3      8       4           115      11
D9V14, multiclass
               clus
vv              PIK3CA MUTATED PIK3CA WILD-TYPE
  CANADA                     2                3
  RUSSIA                     2                8
  UKRAINE                    2                4
  UNITED STATES             44              115
  VIETNAM                    3               11
[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               G1 G2 G3 G4 GX
  PIK3CA MUTATED    6 28 17  1  1
  PIK3CA WILD-TYPE  8 60 65  0  7
D9V15, 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"
D9V16, continuous
D9V17, continuous
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  PIK3CA MUTATED                                             7
  PIK3CA WILD-TYPE                                          19
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  PIK3CA MUTATED                                        3
  PIK3CA WILD-TYPE                                      5
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  PIK3CA MUTATED                                                 0
  PIK3CA WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  PIK3CA MUTATED                7                  30
  PIK3CA WILD-TYPE             30                  63
D9V18, multiclass
                                                 clus
vv                                                PIK3CA MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               7
  LIFELONG NON-SMOKER                                         30
                                                 clus
vv                                                PIK3CA WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                30
  LIFELONG NON-SMOKER                                           63
[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"
D9V19, continuous
D9V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  PIK3CA MUTATED             6       18             0        0        3
  PIK3CA WILD-TYPE          14       36            12        1        4
D9V21, multiclass
               clus
vv              PIK3CA MUTATED PIK3CA WILD-TYPE
  COMBINATION                6               14
  EXTERNAL                  18               36
  EXTERNAL BEAM              0               12
  IMPLANTS                   0                1
  INTERNAL                   3                4
[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"
D9V22, 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
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  PIK3CA MUTATED                    1                0                   8
  PIK3CA WILD-TYPE                  1                2                  12
                  vv
clus               REGIONAL SITE
  PIK3CA MUTATED               3
  PIK3CA WILD-TYPE             1
D9V23, multiclass
                     clus
vv                    PIK3CA MUTATED PIK3CA WILD-TYPE
  DISTANT RECURRENCE               1                1
  LOCAL RECURRENCE                 0                2
  PRIMARY TUMOR FIELD              8               12
  REGIONAL SITE                    3                1
[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"
D9V24, binary
                  cls
clus               0 1
  PIK3CA MUTATED   8 2
  PIK3CA WILD-TYPE 8 2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    2
  PIK3CA WILD-TYPE    8    2
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  CGY              8                8
  GY               2                2
[1] 2 2
[1] FALSE
D9V25, continuous
D9V26, continuous
D9V27, continuous
D9V28, continuous
D9V29, continuous
D9V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  PIK3CA MUTATED                                     1
  PIK3CA WILD-TYPE                                   1
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  PIK3CA MUTATED                                     2                       5
  PIK3CA WILD-TYPE                                   5                      23
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  PIK3CA MUTATED                         1                       3
  PIK3CA WILD-TYPE                       0                       3
D9V31, multiclass
                                     clus
vv                                    PIK3CA MUTATED PIK3CA WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              1                1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              2                5
  OTHER LOCATION, SPECIFY                          5               23
  POSITIVE BLADDER MARGIN                          1                0
  POSITIVE VAGINAL MARGIN                          3                3
[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                                             2
                  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
D9V32, 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)                                                               2
  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"
D9V33, 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
D9V34, continuous
D9V35, continuous
D9V36, 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
D9V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  PIK3CA MUTATED              2           9         11
  PIK3CA WILD-TYPE            6          34         35
D9V38, 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"
D9V39, continuous
D9V40, 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             1         2     0
  PIK3CA WILD-TYPE           1        14     1
D9V41, multiclass
             clus
vv            PIK3CA MUTATED PIK3CA WILD-TYPE
  CARBOPLATIN              1                1
  CISPLATIN                2               14
  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"
D9V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  PIK3CA MUTATED      0   6   11    9  2   2    1    2   5  1   0  2  1
  PIK3CA WILD-TYPE    1  15   49   13  2   5    5    8   8  0   2  0  8
D9V43, multiclass
      clus
vv     PIK3CA MUTATED PIK3CA WILD-TYPE
  T1A1              0                1
  T1B               6               15
  T1B1             11               49
  T1B2              9               13
  T2                2                2
  T2A               2                5
  T2A1              1                5
  T2A2              2                8
  T2B               5                8
  T3                1                0
  T3B               0                2
  T4                2                0
  TX                1                8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V44, 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
D9V45, 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(10) Variable = NFE2L2 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     7   5
  NFE2L2 WILD-TYPE 143  35
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              178 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               5               35 
$`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       195.85 

$`NFE2L2 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       53.16        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-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        58.88        50.76        44.94        40.04        87.75 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       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        12.36        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        14.50        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        14.50        26.01        12.66        12.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.35         1.32         1.97         1.12        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       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q8 
       24.56        21.44        20.48        28.37        21.11        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        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        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
        3.88        11.67        93.99        26.01 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            8.28             0.03 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          195.85           210.67 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           39.96            18.38 
[1] "8.3 - 195.8 (40.0)" "0.0 - 210.7 (18.4)"
[1] "hr=" "1.1"
D10V2, continuous
                  vv
clus                T1  T2 T3+T4
  NFE2L2 MUTATED     4   3     1
  NFE2L2 WILD-TYPE 100  37     4
D10V3, 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"
D10V4, 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
D10V5, 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
                  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                                  22
                  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                                            3
D10V6, 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               22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D10V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     4   8
  NFE2L2 WILD-TYPE  28 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    8
  NFE2L2 WILD-TYPE   28  154
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               4               28
  YES              8              154
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, 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
D10V10, 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"
D10V11, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2   8
  NFE2L2 WILD-TYPE  12 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2    8
  NFE2L2 WILD-TYPE   12  126
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  2               12
  NOT HISPANIC OR LATINO              8              126
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    7  3
  NFE2L2 WILD-TYPE 90 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      7    3
  NFE2L2 WILD-TYPE   90   28
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  TUMOR FREE              7               90
  WITH TUMOR              3               28
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  NFE2L2 MUTATED        0      0       0            12       0
  NFE2L2 WILD-TYPE      5     10       6           147      14
D10V14, multiclass
               clus
vv              NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    0                6
  UNITED STATES             12              147
  VIETNAM                    0               14
[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               G1 G2 G3 G4 GX
  NFE2L2 MUTATED    1  7  3  1  0
  NFE2L2 WILD-TYPE 13 81 79  0  8
D10V15, 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"
D10V16, continuous
D10V17, continuous
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  NFE2L2 MUTATED                                             4
  NFE2L2 WILD-TYPE                                          22
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  NFE2L2 MUTATED                                        1
  NFE2L2 WILD-TYPE                                      7
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  NFE2L2 MUTATED                                                 0
  NFE2L2 WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  NFE2L2 MUTATED                3                   3
  NFE2L2 WILD-TYPE             34                  90
D10V18, multiclass
                                                 clus
vv                                                NFE2L2 MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               3
  LIFELONG NON-SMOKER                                          3
                                                 clus
vv                                                NFE2L2 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                34
  LIFELONG NON-SMOKER                                           90
[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"
D10V19, continuous
D10V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  NFE2L2 MUTATED             3        2             2        0        0
  NFE2L2 WILD-TYPE          17       52            10        1        7
D10V21, multiclass
               clus
vv              NFE2L2 MUTATED NFE2L2 WILD-TYPE
  COMBINATION                3               17
  EXTERNAL                   2               52
  EXTERNAL BEAM              2               10
  IMPLANTS                   0                1
  INTERNAL                   0                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"
D10V22, 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
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  NFE2L2 MUTATED                    0                0                   2
  NFE2L2 WILD-TYPE                  2                2                  18
                  vv
clus               REGIONAL SITE
  NFE2L2 MUTATED               0
  NFE2L2 WILD-TYPE             4
D10V23, multiclass
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2               26 
      TCGA-C5-A0TN       TCGA-C5-A1BF       TCGA-C5-A1BQ       TCGA-C5-A2LZ 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7CO 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-C5-A7UH       TCGA-C5-A7X3       TCGA-DG-A2KL 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DS-A7WF       TCGA-EA-A43B       TCGA-EA-A5FO       TCGA-EX-A3L1 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-FU-A23L       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-HM-A3JJ 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-IR-A3LF       TCGA-JW-A5VG       TCGA-JX-A5QV 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-R2-A69V       TCGA-WL-A834 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
D10V24, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    2  0
  NFE2L2 WILD-TYPE 14  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2    0
  NFE2L2 WILD-TYPE   14    4
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CGY              2               14
  GY               0                4
[1] 2 2
[1] FALSE
D10V25, continuous
D10V26, continuous
D10V27, continuous
D10V28, continuous
D10V29, continuous
D10V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  NFE2L2 MUTATED                                     0
  NFE2L2 WILD-TYPE                                   2
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  NFE2L2 MUTATED                                     0                       2
  NFE2L2 WILD-TYPE                                   7                      26
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  NFE2L2 MUTATED                         0                       2
  NFE2L2 WILD-TYPE                       1                       4
D10V31, multiclass
                                     clus
vv                                    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              0                2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              0                7
  OTHER LOCATION, SPECIFY                          2               26
  POSITIVE BLADDER MARGIN                          0                1
  POSITIVE VAGINAL MARGIN                          2                4
[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                                             2
                  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
D10V32, 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)                                                               2
  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"
D10V33, 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
D10V34, continuous
D10V35, continuous
D10V36, 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
D10V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  NFE2L2 MUTATED              0           4          3
  NFE2L2 WILD-TYPE            8          39         43
D10V38, 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"
D10V39, continuous
D10V40, 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         3     0
  NFE2L2 WILD-TYPE           2        13     1
D10V41, multiclass
             clus
vv            NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CARBOPLATIN              0                2
  CISPLATIN                3               13
  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"
D10V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  NFE2L2 MUTATED      0   0    2    2  0   0    1    0   2  1   0  0  0
  NFE2L2 WILD-TYPE    1  21   58   20  4   7    5   10  11  0   2  2  9
D10V43, multiclass
      clus
vv     NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1A1              0                1
  T1B               0               21
  T1B1              2               58
  T1B2              2               20
  T2                0                4
  T2A               0                7
  T2A1              1                5
  T2A2              0               10
  T2B               2               11
  T3                1                0
  T3B               0                2
  T4                0                2
  TX                0                9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V44, 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
D10V45, 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(11) Variable = FAT2 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  FAT2 MUTATED     9   2
  FAT2 WILD-TYPE 141  38
  FAT2 MUTATED FAT2 WILD-TYPE 
            11            179 
  FAT2 MUTATED FAT2 WILD-TYPE 
             2             38 
$`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        13.58         1.51         1.58 
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-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      134.33        15.48        20.35       147.35        17.19       131.11 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        9.34         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       87.75        36.76         2.66       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 
       12.36        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        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       15.02        14.99        14.96        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64        19.27         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        47.77         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         8.32         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17        31.36        36.26         1.45         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       24.56        21.44        20.48        28.37         8.28        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      195.85        30.31         7.99        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        13.87        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        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  FAT2 MUTATED FAT2 WILD-TYPE 
          1.51           0.03 
  FAT2 MUTATED FAT2 WILD-TYPE 
        155.77         210.67 
  FAT2 MUTATED FAT2 WILD-TYPE 
         29.85          19.59 
[1] "1.5 - 155.8 (29.9)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.7"
D11V2, continuous
                vv
clus              T1  T2 T3+T4
  FAT2 MUTATED     4   3     0
  FAT2 WILD-TYPE 100  37     5
D11V3, 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"
D11V4, 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
D11V5, 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
                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                                  22
                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                                            3
D11V6, 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             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D11V7, binary
                cls
clus               0   1
  FAT2 MUTATED     2   9
  FAT2 WILD-TYPE  30 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      2    9
  FAT2 WILD-TYPE   30  153
     clus
vv    FAT2 MUTATED FAT2 WILD-TYPE
  NO             2             30
  YES            9            153
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, 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
D11V10, 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"
D11V11, binary
                cls
clus               0   1
  FAT2 MUTATED     2   4
  FAT2 WILD-TYPE  12 130
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      2    4
  FAT2 WILD-TYPE   12  130
                        clus
vv                       FAT2 MUTATED FAT2 WILD-TYPE
  HISPANIC OR LATINO                2             12
  NOT HISPANIC OR LATINO            4            130
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                cls
clus              0  1
  FAT2 MUTATED    8  1
  FAT2 WILD-TYPE 89 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      8    1
  FAT2 WILD-TYPE   89   30
            clus
vv           FAT2 MUTATED FAT2 WILD-TYPE
  TUMOR FREE            8             89
  WITH TUMOR            1             30
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  FAT2 MUTATED        0      0       0            10       1
  FAT2 WILD-TYPE      5     10       6           149      13
D11V14, multiclass
               clus
vv              FAT2 MUTATED FAT2 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   0             10
  UKRAINE                  0              6
  UNITED STATES           10            149
  VIETNAM                  1             13
[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             G1 G2 G3 G4 GX
  FAT2 MUTATED    1  4  4  1  1
  FAT2 WILD-TYPE 13 84 78  0  7
D11V15, 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"
D11V16, continuous
[1] "Remove cluster labels:" "FAT2 MUTATED"          
clus
  FAT2 MUTATED FAT2 WILD-TYPE 
             1             28 
    TCGA-BI-A0VR     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1BQ 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A2M2 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DG-A2KK 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-EK-A2RA     TCGA-EX-A69M     TCGA-FU-A2QG 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-FU-A3TX     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" 
D11V17, continuous
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  FAT2 MUTATED                                             1
  FAT2 WILD-TYPE                                          25
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  FAT2 MUTATED                                        0
  FAT2 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  FAT2 MUTATED                                                 0              4
  FAT2 WILD-TYPE                                               1             33
                vv
clus             LIFELONG NON-SMOKER
  FAT2 MUTATED                     5
  FAT2 WILD-TYPE                  88
D11V18, multiclass
                                                 clus
vv                                                FAT2 MUTATED FAT2 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                1             25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             4             33
  LIFELONG NON-SMOKER                                        5             88
[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"
D11V19, continuous
D11V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  FAT2 MUTATED             1        5             1        0        0
  FAT2 WILD-TYPE          19       49            11        1        7
D11V21, multiclass
               clus
vv              FAT2 MUTATED FAT2 WILD-TYPE
  COMBINATION              1             19
  EXTERNAL                 5             49
  EXTERNAL BEAM            1             11
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D11V22, 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
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  FAT2 MUTATED                    0                0                   2
  FAT2 WILD-TYPE                  2                2                  18
                vv
clus             REGIONAL SITE
  FAT2 MUTATED               0
  FAT2 WILD-TYPE             4
D11V23, multiclass
[1] "Remove cluster labels:" "FAT2 MUTATED"          
clus
  FAT2 MUTATED FAT2 WILD-TYPE 
             2             26 
    TCGA-C5-A0TN     TCGA-C5-A1BF     TCGA-C5-A1BQ     TCGA-C5-A2LZ 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DS-A7WF 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A5FO     TCGA-EX-A3L1     TCGA-FU-A23L 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A4S6 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-JW-A5VG     TCGA-JX-A3Q0     TCGA-JX-A5QV 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-WL-A834 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
D11V24, binary
                cls
clus              0  1
  FAT2 MUTATED    1  0
  FAT2 WILD-TYPE 15  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT2 MUTATED      1    0
  FAT2 WILD-TYPE   15    4
     clus
vv    FAT2 MUTATED FAT2 WILD-TYPE
  CGY            1             15
  GY             0              4
[1] 2 2
[1] FALSE
D11V25, continuous
D11V26, continuous
D11V27, continuous
D11V28, continuous
D11V29, continuous
D11V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  FAT2 MUTATED                                     0
  FAT2 WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  FAT2 MUTATED                                     1                       1
  FAT2 WILD-TYPE                                   6                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  FAT2 MUTATED                         0                       1
  FAT2 WILD-TYPE                       1                       5
D11V31, multiclass
                                     clus
vv                                    FAT2 MUTATED FAT2 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            1              6
  OTHER LOCATION, SPECIFY                        1             27
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              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)
  FAT2 MUTATED                                               0
  FAT2 WILD-TYPE                                             2
                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
D11V32, 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)                                                             2
  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"
D11V33, 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
D11V34, continuous
D11V35, continuous
D11V36, 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
D11V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  FAT2 MUTATED              0           3          2
  FAT2 WILD-TYPE            8          40         44
D11V38, 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"
D11V39, continuous
D11V40, 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         2     0
  FAT2 WILD-TYPE           2        14     1
D11V41, multiclass
[1] "Remove cluster labels:" "FAT2 MUTATED"          
clus
  FAT2 MUTATED FAT2 WILD-TYPE 
             2             17 
    TCGA-C5-A1BE     TCGA-C5-A1BI     TCGA-C5-A1BN     TCGA-C5-A1M9 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MK     TCGA-C5-A1MQ 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A3HD 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EK-A2H0     TCGA-EK-A2H1 
"FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" "FAT2 WILD-TYPE" 
    TCGA-HM-A3JJ 
"FAT2 WILD-TYPE" 
D11V42, 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" 
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  FAT2 MUTATED      0   0    2    2  0   0    1    0   2  0   0  0  1
  FAT2 WILD-TYPE    1  21   58   20  4   7    5   10  11  1   2  2  8
D11V43, multiclass
      clus
vv     FAT2 MUTATED FAT2 WILD-TYPE
  T1A1            0              1
  T1B             0             21
  T1B1            2             58
  T1B2            2             20
  T2              0              4
  T2A             0              7
  T2A1            1              5
  T2A2            0             10
  T2B             2             11
  T3              0              1
  T3B             0              2
  T4              0              2
  TX              1              8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V44, 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
D11V45, 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(12) Variable = ZNF750 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED     7   2
  ZNF750 WILD-TYPE 143  38
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              181 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               38 
$`ZNF750 MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1MH TCGA-C5-A3HE TCGA-DR-A0ZM TCGA-FU-A3TQ TCGA-JW-A5VL 
       19.86        38.99        18.02        58.88         1.58        15.58 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-Q1-A73O 
        0.30         0.82        14.07 

$`ZNF750 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        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-A3HF 
       78.35       100.14        38.43        33.24        52.01        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        58.88        50.76        44.94        40.04        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76         2.66       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        12.36 
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 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51        19.27         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX 
        0.92         2.17        31.36        36.26         1.45         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         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       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       20.48        28.37         8.28        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A51Y 
        7.99        11.28         0.89        12.49        13.35        13.87 
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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
            0.30             0.03 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           58.88           210.67 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           15.58            20.35 
[1] "0.3 - 58.9 (15.6)"  "0.0 - 210.7 (20.4)"
[1] "hr=" "1.8"
D12V2, continuous
                  vv
clus                T1  T2 T3+T4
  ZNF750 MUTATED     4   3     0
  ZNF750 WILD-TYPE 100  37     5
D12V3, 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"
D12V4, 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
D12V5, 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
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ZNF750 MUTATED               0                                9
  ZNF750 WILD-TYPE             4                              149
                  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                                  22
                  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                                            3
D12V6, multiclass
                                               clus
vv                                              ZNF750 MUTATED ZNF750 WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           9              149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              1                4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        0               22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D12V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     2   8
  ZNF750 WILD-TYPE  30 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    8
  ZNF750 WILD-TYPE   30  154
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               2               30
  YES              8              154
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, 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     5
  ZNF750 WILD-TYPE                                         1   133
D12V10, 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                                                  5              133
[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
  ZNF750 MUTATED     2   8
  ZNF750 WILD-TYPE  12 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    8
  ZNF750 WILD-TYPE   12  126
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  2               12
  NOT HISPANIC OR LATINO              8              126
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                  cls
clus                0  1
  ZNF750 MUTATED    4  1
  ZNF750 WILD-TYPE 93 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      4    1
  ZNF750 WILD-TYPE   93   30
            clus
vv           ZNF750 MUTATED ZNF750 WILD-TYPE
  TUMOR FREE              4               93
  WITH TUMOR              1               30
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  ZNF750 MUTATED        0      0       0             7       3
  ZNF750 WILD-TYPE      5     10       6           152      11
D12V14, multiclass
               clus
vv              ZNF750 MUTATED ZNF750 WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    0                6
  UNITED STATES              7              152
  VIETNAM                    3               11
[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               G1 G2 G3 G4 GX
  ZNF750 MUTATED    1  4  4  0  1
  ZNF750 WILD-TYPE 13 84 78  1  7
D12V15, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  G1              1               13
  G2              4               84
  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"
D12V16, continuous
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               27 
      TCGA-BI-A0VR       TCGA-C5-A1BJ       TCGA-C5-A1BL       TCGA-C5-A1ME 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A2M2       TCGA-C5-A3HD       TCGA-C5-A7CM 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-DG-A2KK       TCGA-DS-A3LQ       TCGA-EK-A2RA 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3TX       TCGA-FU-A3WB 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-IR-A3L7       TCGA-IR-A3LB 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JX-A3Q0       TCGA-MU-A5YI       TCGA-Q1-A6DW 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
D12V17, continuous
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  ZNF750 MUTATED                                             1
  ZNF750 WILD-TYPE                                          25
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  ZNF750 MUTATED                                        1
  ZNF750 WILD-TYPE                                      7
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  ZNF750 MUTATED                                                 0
  ZNF750 WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  ZNF750 MUTATED                2                   6
  ZNF750 WILD-TYPE             35                  87
D12V18, multiclass
                                                 clus
vv                                                ZNF750 MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               2
  LIFELONG NON-SMOKER                                          6
                                                 clus
vv                                                ZNF750 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                35
  LIFELONG NON-SMOKER                                           87
[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"
D12V19, continuous
D12V20, continuous
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               80 
      TCGA-C5-A0TN       TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BI 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1BJ       TCGA-C5-A1BL       TCGA-C5-A1M6       TCGA-C5-A1M8 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1ML       TCGA-C5-A1MQ       TCGA-C5-A2LT       TCGA-C5-A2LX 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A2LY       TCGA-C5-A2LZ       TCGA-C5-A3HD       TCGA-C5-A3HF 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7UE       TCGA-C5-A7UH 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KL 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DG-A2KM       TCGA-DS-A0VK       TCGA-DS-A0VN       TCGA-DS-A1OA 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-DS-A5RQ       TCGA-DS-A7WH       TCGA-DS-A7WI 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EA-A3QD       TCGA-EA-A3Y4       TCGA-EA-A43B       TCGA-EA-A44S 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EA-A4BA       TCGA-EA-A5FO       TCGA-EA-A5O9       TCGA-EK-A2H0 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EX-A3L1       TCGA-EX-A449       TCGA-FU-A23L       TCGA-FU-A3HY 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-FU-A3HZ       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LK       TCGA-IR-A3LL       TCGA-JW-A5VG       TCGA-JW-A5VH 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-JW-A5VI       TCGA-JX-A5QV       TCGA-LP-A4AU       TCGA-LP-A4AX 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-LP-A7HU       TCGA-MU-A5YI       TCGA-MY-A5BD       TCGA-MY-A5BF 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-Q1-A5R2       TCGA-Q1-A5R3       TCGA-Q1-A6DW       TCGA-Q1-A73Q 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-Q1-A73S       TCGA-R2-A69V       TCGA-RA-A741       TCGA-WL-A834 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  ZNF750 MUTATED             1        3             1        0        0
  ZNF750 WILD-TYPE          19       51            11        1        7
D12V21, multiclass
               clus
vv              ZNF750 MUTATED ZNF750 WILD-TYPE
  COMBINATION                1               19
  EXTERNAL                   3               51
  EXTERNAL BEAM              1               11
  IMPLANTS                   0                1
  INTERNAL                   0                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"
D12V22, binary
                  cls
clus                0  1
  ZNF750 MUTATED    2  0
  ZNF750 WILD-TYPE 24  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    0
  ZNF750 WILD-TYPE   24    3
                         clus
vv                        ZNF750 MUTATED ZNF750 WILD-TYPE
  COMPLETED AS PLANNED                 2               24
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  ZNF750 MUTATED                    0                0                   1
  ZNF750 WILD-TYPE                  2                2                  19
                  vv
clus               REGIONAL SITE
  ZNF750 MUTATED               0
  ZNF750 WILD-TYPE             4
D12V23, multiclass
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               1               27 
      TCGA-C5-A0TN       TCGA-C5-A1BF       TCGA-C5-A2LZ       TCGA-C5-A7CK 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-C5-A7UE 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7UH       TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DS-A7WF 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EA-A43B       TCGA-EA-A5FO       TCGA-EX-A3L1       TCGA-FU-A23L 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-HM-A3JJ       TCGA-HM-A4S6 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-JW-A5VG       TCGA-JX-A3Q0 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-JX-A5QV       TCGA-R2-A69V       TCGA-WL-A834 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
D12V24, binary
                  cls
clus                0  1
  ZNF750 MUTATED    0  0
  ZNF750 WILD-TYPE 16  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0    0
  ZNF750 WILD-TYPE   16    4
D12V25, continuous
D12V26, continuous
D12V27, continuous
D12V28, continuous
D12V29, continuous
D12V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ZNF750 MUTATED                                     0
  ZNF750 WILD-TYPE                                   2
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ZNF750 MUTATED                                     0                       2
  ZNF750 WILD-TYPE                                   7                      26
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ZNF750 MUTATED                         0                       0
  ZNF750 WILD-TYPE                       1                       6
D12V31, multiclass
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               42 
      TCGA-BI-A20A       TCGA-C5-A0TN       TCGA-C5-A1BE       TCGA-C5-A1BK 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MJ 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS       TCGA-C5-A2LT 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2M1       TCGA-C5-A3HL 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A7CG       TCGA-C5-A7CJ       TCGA-C5-A7UC       TCGA-DG-A2KL 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EA-A50E       TCGA-EK-A2RN 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EK-A2RO       TCGA-EX-A1H5       TCGA-EX-A449       TCGA-FU-A3EO 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LK 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ZNF750 MUTATED                                               0
  ZNF750 WILD-TYPE                                             2
                  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                                                                                   4
  ZNF750 WILD-TYPE                                                                                56
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ZNF750 MUTATED                                                                                              4
  ZNF750 WILD-TYPE                                                                                           84
D12V32, 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)                         4
  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)                                                               2
  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)               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"
D12V33, 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
D12V34, continuous
D12V35, continuous
D12V36, binary
                  cls
clus                0  1
  ZNF750 MUTATED    2  6
  ZNF750 WILD-TYPE 37 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2    6
  ZNF750 WILD-TYPE   37   80
                                          clus
vv                                         ZNF750 MUTATED ZNF750 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  2               37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              6               80
[1] 2 2
[1] FALSE
D12V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  ZNF750 MUTATED              0           1          2
  ZNF750 WILD-TYPE            8          42         44
D12V38, 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"
D12V39, continuous
D12V40, 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         2     0
  ZNF750 WILD-TYPE           2        14     1
D12V41, multiclass
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               17 
      TCGA-C5-A1BE       TCGA-C5-A1BI       TCGA-C5-A1BN       TCGA-C5-A1M9 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-C5-A1MQ 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A3HD 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EK-A2H0       TCGA-EK-A2H1 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-HM-A3JJ 
"ZNF750 WILD-TYPE" 
D12V42, continuous
[1] "Remove cluster labels:" "ZNF750 MUTATED"        
clus
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               1                9 
      TCGA-C5-A1BN       TCGA-C5-A1ML       TCGA-C5-A1MN       TCGA-C5-A1MP 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-EK-A2RO       TCGA-HM-A3JK       TCGA-JW-A852       TCGA-JX-A3Q8 
"ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" "ZNF750 WILD-TYPE" 
      TCGA-MU-A51Y 
"ZNF750 WILD-TYPE" 
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  ZNF750 MUTATED      0   1    1    2  0   1    0    0   2  0   0  0  1
  ZNF750 WILD-TYPE    1  20   59   20  4   6    6   10  11  1   2  2  8
D12V43, multiclass
      clus
vv     ZNF750 MUTATED ZNF750 WILD-TYPE
  T1A1              0                1
  T1B               1               20
  T1B1              1               59
  T1B2              2               20
  T2                0                4
  T2A               1                6
  T2A1              0                6
  T2A2              0               10
  T2B               2               11
  T3                0                1
  T3B               0                2
  T4                0                2
  TX                1                8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V44, 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          5         0         0
  ZNF750 WILD-TYPE         1         24         2         5
D12V45, 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              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(13) Variable = BAP1 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED     3   1
  BAP1 WILD-TYPE 147  39
  BAP1 MUTATED BAP1 WILD-TYPE 
             4            186 
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             39 
$`BAP1 MUTATED`
TCGA-C5-A1BM TCGA-EA-A44S TCGA-EK-A2RB TCGA-EK-A2RC 
       82.85        12.66         0.07         4.04 

$`BAP1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        26.01        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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       117.40        96.95        78.71 
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-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       21.44        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 
      195.85        30.31         7.99        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        13.87        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        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.07           0.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
         82.85         210.67 
  BAP1 MUTATED BAP1 WILD-TYPE 
         8.350         19.825 
[1] "0.1 - 82.8 (8.3)"   "0.0 - 210.7 (19.8)"
[1] "hr=" "1.6"
D13V2, continuous
                vv
clus              T1  T2 T3+T4
  BAP1 MUTATED     0   2     0
  BAP1 WILD-TYPE 104  38     5
D13V3, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            147 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BK     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-A3HE     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-DG-A2KH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"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-A439 
"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-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD     TCGA-EA-A5ZE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R     TCGA-EK-A2IP 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9     TCGA-EK-A2RA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RJ     TCGA-EK-A2RK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RL     TCGA-EK-A2RN     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A449 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-EX-A69M     TCGA-FU-A23K     TCGA-FU-A23L 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3NI     TCGA-FU-A3TQ     TCGA-FU-A3TX     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" 
D13V4, 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
D13V5, 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
                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                                  22
                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                                            3
D13V6, 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             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D13V7, binary
                cls
clus               0   1
  BAP1 MUTATED     1   3
  BAP1 WILD-TYPE  31 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    3
  BAP1 WILD-TYPE   31  159
     clus
vv    BAP1 MUTATED BAP1 WILD-TYPE
  NO             1             31
  YES            3            159
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            119 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M5     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-A1MI     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-A2LY     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UC     TCGA-C5-A7UE     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-A3Y4     TCGA-EA-A410 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A411     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-A6QX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RO     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-EX-A69M 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     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-A3NI     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TX     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
D13V10, 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"
D13V11, binary
                cls
clus               0   1
  BAP1 MUTATED     0   2
  BAP1 WILD-TYPE  14 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    2
  BAP1 WILD-TYPE   14  132
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            2            132
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                cls
clus              0  1
  BAP1 MUTATED    1  0
  BAP1 WILD-TYPE 96 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1    0
  BAP1 WILD-TYPE   96   31
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  TUMOR FREE            1             96
  WITH TUMOR            0             31
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  BAP1 MUTATED        0      0       1             3       0
  BAP1 WILD-TYPE      5     10       5           156      14
D13V14, multiclass
               clus
vv              BAP1 MUTATED BAP1 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   0             10
  UKRAINE                  1              5
  UNITED STATES            3            156
  VIETNAM                  0             14
[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             G1 G2 G3 G4 GX
  BAP1 MUTATED    0  2  2  0  0
  BAP1 WILD-TYPE 14 86 80  1  8
D13V15, 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"
D13V16, continuous
D13V17, continuous
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  BAP1 MUTATED                                             1
  BAP1 WILD-TYPE                                          25
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  BAP1 MUTATED                                        0
  BAP1 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  BAP1 MUTATED                                                 0              1
  BAP1 WILD-TYPE                                               1             36
                vv
clus             LIFELONG NON-SMOKER
  BAP1 MUTATED                     1
  BAP1 WILD-TYPE                  92
D13V18, multiclass
                                                 clus
vv                                                BAP1 MUTATED BAP1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                1             25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             1             36
  LIFELONG NON-SMOKER                                        1             92
[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"
D13V19, continuous
D13V20, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             81 
    TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1M6     TCGA-C5-A1M8 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MQ     TCGA-C5-A2LT     TCGA-C5-A2LX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A3HD     TCGA-C5-A3HF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7UE     TCGA-C5-A7UH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7X3     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-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A3QD     TCGA-EA-A3Y4     TCGA-EA-A43B 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EK-A2H0 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-FU-A23L     TCGA-FU-A3HY 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB 
"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-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BF 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73Q     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-WL-A834 
"BAP1 WILD-TYPE" 
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  BAP1 MUTATED             1        1             0        0        0
  BAP1 WILD-TYPE          19       53            12        1        7
D13V21, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             92 
    TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M8     TCGA-C5-A1M9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MQ     TCGA-C5-A2LT 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A3HD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     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-A2KJ     TCGA-DG-A2KK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"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-A7WH     TCGA-DS-A7WI     TCGA-EA-A3QD     TCGA-EA-A3Y4 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A4BA     TCGA-EA-A5FO     TCGA-EA-A5O9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EX-A3L1     TCGA-EX-A449     TCGA-FU-A23L 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     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-JX-A3Q0     TCGA-JX-A5QV 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AU     TCGA-LP-A4AX     TCGA-LP-A7HU     TCGA-MU-A5YI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D13V22, 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
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  BAP1 MUTATED                    0                0                   0
  BAP1 WILD-TYPE                  2                2                  20
                vv
clus             REGIONAL SITE
  BAP1 MUTATED               0
  BAP1 WILD-TYPE             4
D13V23, multiclass
D13V24, binary
                cls
clus              0  1
  BAP1 MUTATED    0  0
  BAP1 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0    0
  BAP1 WILD-TYPE   16    4
D13V25, continuous
D13V26, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             99 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     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-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     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-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     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-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     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-A556     TCGA-EA-A5O9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A449     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" 
D13V27, 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" 
D13V28, continuous
D13V29, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            107 
    TCGA-BI-A0VS     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     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-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     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-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     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-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"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-A4BA 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5O9     TCGA-EA-A6QX     TCGA-EK-A2RN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H6     TCGA-EX-A449     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" 
D13V30, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            101 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     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-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     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-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     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-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     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-A556     TCGA-EA-A5O9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69M     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                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  BAP1 MUTATED                                     0                       0
  BAP1 WILD-TYPE                                   7                      28
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  BAP1 MUTATED                         0                       1
  BAP1 WILD-TYPE                       1                       5
D13V31, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             43 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M5     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-A1MJ     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-A2M1     TCGA-C5-A3HE     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-DG-A2KL 
"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-EA-A50E 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EX-A1H5     TCGA-EX-A449 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-HM-A4S6     TCGA-IR-A3LH     TCGA-IR-A3LI 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IR-A3LK     TCGA-UC-A7PD     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  BAP1 MUTATED                                               0
  BAP1 WILD-TYPE                                             2
                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
D13V32, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            158 
    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-A2GZ     TCGA-EK-A2H0     TCGA-EK-A2H1     TCGA-EK-A2PG 
"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-A449     TCGA-EX-A69L     TCGA-EX-A69M     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-A3TX 
"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-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A5R3     TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73O     TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D13V33, 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
D13V34, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            119 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BL 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1M5     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-A1MI     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-A2LY     TCGA-C5-A2M1 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7UC     TCGA-C5-A7UE     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-A3Y4     TCGA-EA-A410 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A411     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-A6QX 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RO     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-EX-A69M 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     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-A3NI     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TX     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" 
D13V35, continuous
D13V36, 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
D13V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  BAP1 MUTATED              0           0          1
  BAP1 WILD-TYPE            8          43         45
D13V38, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             96 
    TCGA-C5-A1BI     TCGA-C5-A1BL     TCGA-C5-A1BN     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-A1MN     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-A2M1     TCGA-C5-A2M2 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7UH 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"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-A3LQ     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-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-A5O9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EK-A2R7     TCGA-EK-A3GK 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A69M     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" 
D13V39, continuous
D13V40, 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           2        16     1
D13V41, multiclass
D13V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  BAP1 MUTATED      0   0    0    0  1   0    0    1   0  0   0  0  0
  BAP1 WILD-TYPE    1  21   60   22  3   7    6    9  13  1   2  2  9
D13V43, multiclass
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2            156 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1M5 
"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-A1MI     TCGA-C5-A1MJ     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-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-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-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-A2IP     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RN     TCGA-EK-A3GJ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EK-A3GN     TCGA-EX-A1H5     TCGA-EX-A1H6 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     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-A3NI     TCGA-FU-A3TQ 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-FU-A3TX     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-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-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-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AW 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BE 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
D13V44, 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
D13V45, 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(14) Variable = RAB35 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  RAB35 MUTATED     2   1
  RAB35 WILD-TYPE 148  39
  RAB35 MUTATED RAB35 WILD-TYPE 
              3             187 
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              39 
$`RAB35 MUTATED`
TCGA-BI-A0VR TCGA-C5-A1MK TCGA-EA-A5ZE 
       49.48         2.43        14.99 

$`RAB35 WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       57.04        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46        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        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       13.91        15.02        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        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-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       195.85        30.31         7.99        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        13.87        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  RAB35 MUTATED RAB35 WILD-TYPE 
           2.43            0.03 
  RAB35 MUTATED RAB35 WILD-TYPE 
          49.48          210.67 
  RAB35 MUTATED RAB35 WILD-TYPE 
          14.99           19.79 
[1] "2.4 - 49.5 (15.0)"  "0.0 - 210.7 (19.8)"
[1] "hr=" "2.2"
D14V2, continuous
                 vv
clus               T1  T2 T3+T4
  RAB35 MUTATED     2   1     0
  RAB35 WILD-TYPE 102  39     5
D14V3, multiclass
       clus
vv      RAB35 MUTATED RAB35 WILD-TYPE
  T1                2             102
  T2                1              39
  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
  RAB35 MUTATED    2  1
  RAB35 WILD-TYPE 93 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      2    1
  RAB35 WILD-TYPE   93   43
   clus
vv  RAB35 MUTATED RAB35 WILD-TYPE
  0             2              93
  1             1              43
[1] 2 2
[1] FALSE
D14V5, binary
                 cls
clus               0  1
  RAB35 MUTATED    3  0
  RAB35 WILD-TYPE 76  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      3    0
  RAB35 WILD-TYPE   76    4
   clus
vv  RAB35 MUTATED RAB35 WILD-TYPE
  0             3              76
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  RAB35 MUTATED               0                                4
  RAB35 WILD-TYPE             4                              154
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  RAB35 MUTATED                                               0
  RAB35 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  RAB35 MUTATED                                     0
  RAB35 WILD-TYPE                                  22
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  RAB35 MUTATED                                           0
  RAB35 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  RAB35 MUTATED                                              0
  RAB35 WILD-TYPE                                            3
D14V6, multiclass
                                               clus
vv                                              RAB35 MUTATED RAB35 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          4             154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D14V7, binary
                 cls
clus                0   1
  RAB35 MUTATED     1   3
  RAB35 WILD-TYPE  31 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      1    3
  RAB35 WILD-TYPE   31  159
     clus
vv    RAB35 MUTATED RAB35 WILD-TYPE
  NO              1              31
  YES             3             159
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              56 
     TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V9, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1             120 
     TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH      TCGA-DG-A2KJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A410 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO      TCGA-EA-A5O9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO      TCGA-EK-A3GK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R1 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A6DV      TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB35 MUTATED                                  0     2
  RAB35 WILD-TYPE                                8    17
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RAB35 MUTATED                           0
  RAB35 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB35 MUTATED                                           0     2
  RAB35 WILD-TYPE                                         1   136
D14V10, multiclass
                                           clus
vv                                          RAB35 MUTATED RAB35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 2              17
  BLACK OR AFRICAN AMERICAN                             0              16
  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"
D14V11, binary
                 cls
clus                0   1
  RAB35 MUTATED     0   4
  RAB35 WILD-TYPE  14 130
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      0    4
  RAB35 WILD-TYPE   14  130
                        clus
vv                       RAB35 MUTATED RAB35 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             4             130
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                 cls
clus               0  1
  RAB35 MUTATED    1  1
  RAB35 WILD-TYPE 96 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      1    1
  RAB35 WILD-TYPE   96   30
            clus
vv           RAB35 MUTATED RAB35 WILD-TYPE
  TUMOR FREE             1              96
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  RAB35 MUTATED        0      0       0             2       2
  RAB35 WILD-TYPE      5     10       6           157      12
D14V14, multiclass
               clus
vv              RAB35 MUTATED RAB35 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             2             157
  VIETNAM                   2              12
[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              G1 G2 G3 G4 GX
  RAB35 MUTATED    0  1  3  0  0
  RAB35 WILD-TYPE 14 87 79  1  8
D14V15, multiclass
    clus
vv   RAB35 MUTATED RAB35 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"
D14V16, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              28 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BQ      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-DS-A3LQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JX-A3Q0      TCGA-MU-A5YI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A6DW      TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V17, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              56 
     TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  RAB35 MUTATED                                             1
  RAB35 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  RAB35 MUTATED                                        0
  RAB35 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  RAB35 MUTATED                                                 0
  RAB35 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  RAB35 MUTATED                0                   3
  RAB35 WILD-TYPE             37                  90
D14V18, multiclass
                                                 clus
vv                                                RAB35 MUTATED RAB35 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              0              37
  LIFELONG NON-SMOKER                                         3              90
[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"
D14V19, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              51 
     TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME      TCGA-C5-A1MF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CL      TCGA-C5-A7CO 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DR-A0ZM      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ      TCGA-FU-A3TX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LB 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK      TCGA-JX-A3Q0 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V20, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              81 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1M6      TCGA-C5-A1M8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1ML 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LZ      TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VN      TCGA-DS-A1OA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WH      TCGA-DS-A7WI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A43B      TCGA-EA-A44S 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A5FO      TCGA-EA-A5O9      TCGA-EK-A2H0 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A3L1      TCGA-EX-A449      TCGA-FU-A23L      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JX-A5QV      TCGA-LP-A4AU      TCGA-LP-A4AX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-LP-A7HU      TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73O 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73Q      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-WL-A834 
"RAB35 WILD-TYPE" 
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  RAB35 MUTATED             1        0             0        0        0
  RAB35 WILD-TYPE          19       54            12        1        7
D14V21, multiclass
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              93 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MQ      TCGA-C5-A2LT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KJ      TCGA-DG-A2KK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A3QD      TCGA-EA-A3Y4 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A5FO 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EK-A2H0      TCGA-EX-A3L1      TCGA-EX-A449 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC      TCGA-IR-A3LF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JX-A3Q0 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AU      TCGA-LP-A4AX      TCGA-LP-A7HU 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73O      TCGA-Q1-A73Q 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-UC-A7PD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-WL-A834 
"RAB35 WILD-TYPE" 
D14V22, binary
                 cls
clus               0  1
  RAB35 MUTATED    0  1
  RAB35 WILD-TYPE 26  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      0    1
  RAB35 WILD-TYPE   26    2
                         clus
vv                        RAB35 MUTATED RAB35 WILD-TYPE
  COMPLETED AS PLANNED                0              26
  TREATMENT NOT COMPLETED             1               2
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  RAB35 MUTATED                    0                0                   0
  RAB35 WILD-TYPE                  2                2                  20
                 vv
clus              REGIONAL SITE
  RAB35 MUTATED               0
  RAB35 WILD-TYPE             4
D14V23, multiclass
D14V24, binary
                 cls
clus               0  1
  RAB35 MUTATED    0  0
  RAB35 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      0    0
  RAB35 WILD-TYPE   16    4
D14V25, continuous
D14V26, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              2              99 
     TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ      TCGA-C5-A1ML 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT      TCGA-EA-A3HU 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A449      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A770      TCGA-HG-A2PA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V27, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              2             108 
     TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EA-A5ZD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2IP      TCGA-EK-A2RK      TCGA-EX-A69L      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770      TCGA-HG-A2PA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7      TCGA-IR-A3LC 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V28, continuous
D14V29, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1             108 
     TCGA-BI-A0VS      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EA-A6QX 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EX-A1H6      TCGA-EX-A449      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-LP-A5U2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MU-A51Y      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V30, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              2             101 
     TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M7 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ      TCGA-C5-A1ML 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT      TCGA-EA-A3HU 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A5XV      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-Q1-A73Q      TCGA-RA-A741      TCGA-UC-A7PD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-UC-A7PF 
"RAB35 WILD-TYPE" 
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  RAB35 MUTATED                                     0
  RAB35 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  RAB35 MUTATED                                     0                       0
  RAB35 WILD-TYPE                                   7                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  RAB35 MUTATED                         0                       0
  RAB35 WILD-TYPE                       1                       6
D14V31, multiclass
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  RAB35 MUTATED                                               0
  RAB35 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  RAB35 MUTATED                                                1
  RAB35 WILD-TYPE                                              9
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  RAB35 MUTATED                                                                                   2
  RAB35 WILD-TYPE                                                                                58
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  RAB35 MUTATED                                                                                              0
  RAB35 WILD-TYPE                                                                                           88
D14V32, multiclass
                                                                                              clus
vv                                                                                             RAB35 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)                        2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             0
                                                                                              clus
vv                                                                                             RAB35 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             9
  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)              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"
D14V33, binary
                 cls
clus               0  1
  RAB35 MUTATED    1  1
  RAB35 WILD-TYPE 62 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      1    1
  RAB35 WILD-TYPE   62   66
         clus
vv        RAB35 MUTATED RAB35 WILD-TYPE
  ABSENT              1              62
  PRESENT             1              66
[1] 2 2
[1] FALSE
D14V34, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1             120 
     TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH      TCGA-DG-A2KJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A410 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO      TCGA-EA-A5O9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO      TCGA-EK-A3GK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R1 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A6DV      TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V35, continuous
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              2             138 
     TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH      TCGA-DG-A2KJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2GZ      TCGA-EK-A2IP 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2PK      TCGA-EK-A2R7      TCGA-EK-A2R8      TCGA-EK-A2R9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EK-A2RC      TCGA-EK-A2RD      TCGA-EK-A2RE 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2RJ      TCGA-EK-A2RK      TCGA-EK-A2RL      TCGA-EK-A2RM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EK-A3GJ      TCGA-EK-A3GK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AW      TCGA-LP-A4AX      TCGA-LP-A5U2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-MU-A5YI      TCGA-MY-A5BD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV      TCGA-Q1-A73P 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-UC-A7PD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-UC-A7PF      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V36, binary
                 cls
clus               0  1
  RAB35 MUTATED    1  2
  RAB35 WILD-TYPE 38 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      1    2
  RAB35 WILD-TYPE   38   84
                                          clus
vv                                         RAB35 MUTATED RAB35 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 1              38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             2              84
[1] 2 2
[1] FALSE
D14V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  RAB35 MUTATED              0           1          0
  RAB35 WILD-TYPE            8          42         46
D14V38, multiclass
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              96 
     TCGA-C5-A1BI      TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M6 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MN      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7UH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KM      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A3QE      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A5ZF      TCGA-EK-A2R7      TCGA-EK-A3GK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A5U2      TCGA-LP-A5U3      TCGA-LP-A7HU 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A5R1      TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DV 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-UC-A7PD      TCGA-WL-A834 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V39, continuous
D14V40, binary
                 cls
clus               0  1
  RAB35 MUTATED    1  1
  RAB35 WILD-TYPE 87 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB35 MUTATED      1    1
  RAB35 WILD-TYPE   87   15
         clus
vv        RAB35 MUTATED RAB35 WILD-TYPE
  ABSENT              1              87
  PRESENT             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  RAB35 MUTATED             1         0     0
  RAB35 WILD-TYPE           1        16     1
D14V41, multiclass
[1] "Remove cluster labels:" "RAB35 MUTATED"         
clus
  RAB35 MUTATED RAB35 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"RAB35 WILD-TYPE" "RAB35 WILD-TYPE" 
D14V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  RAB35 MUTATED      0   1    1    0  0   0    0    0   1  0   0  0  0
  RAB35 WILD-TYPE    1  20   59   22  4   7    6   10  12  1   2  2  9
D14V43, multiclass
      clus
vv     RAB35 MUTATED RAB35 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             1              59
  T1B2             0              22
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              1              12
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  RAB35 MUTATED         0        0         0         0        1         1
  RAB35 WILD-TYPE       4        1         1         1       27        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  RAB35 MUTATED           0        0         0          0          0         0
  RAB35 WILD-TYPE        29        4         6          5          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  RAB35 MUTATED           0          2         0         0
  RAB35 WILD-TYPE         1         27         2         5
D14V45, multiclass
            clus
vv           RAB35 MUTATED RAB35 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             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(15) Variable = ERBB3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED     7   3
  ERBB3 WILD-TYPE 143  37
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             10             180 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              3              37 
$`ERBB3 MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2M2 TCGA-C5-A7CO TCGA-EA-A411 TCGA-EA-A5FO 
       35.61         0.46        33.24       147.35        24.56        26.79 
TCGA-EK-A3GK TCGA-IR-A3LH TCGA-Q1-A73O TCGA-Q1-A73R 
        0.10        78.71        14.07        15.39 

$`ERBB3 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       57.73        53.16        38.99         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-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        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-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH 
       20.35        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 
       58.88        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76         2.66       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        12.36 
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-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50        26.40        14.50        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        7.46        14.89        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         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-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        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       195.85        30.31         7.99        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        13.87 
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-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.10            0.03 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         147.35          210.67 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         25.675          19.475 
[1] "0.1 - 147.3 (25.7)" "0.0 - 210.7 (19.5)"
[1] "hr=" "1.3"
D15V2, continuous
                 vv
clus              T1 T2 T3+T4
  ERBB3 MUTATED    5  1     0
  ERBB3 WILD-TYPE 99 39     5
D15V3, multiclass
       clus
vv      ERBB3 MUTATED ERBB3 WILD-TYPE
  T1                5              99
  T2                1              39
  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
  ERBB3 MUTATED    5  1
  ERBB3 WILD-TYPE 90 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      5    1
  ERBB3 WILD-TYPE   90   43
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0             5              90
  1             1              43
[1] 2 2
[1] FALSE
D15V5, binary
                 cls
clus               0  1
  ERBB3 MUTATED    4  0
  ERBB3 WILD-TYPE 75  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      4    0
  ERBB3 WILD-TYPE   75    4
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0             4              75
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ERBB3 MUTATED               0                                6
  ERBB3 WILD-TYPE             4                              152
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  ERBB3 MUTATED                                               0
  ERBB3 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  ERBB3 MUTATED                                     5
  ERBB3 WILD-TYPE                                  17
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  ERBB3 MUTATED                                           0
  ERBB3 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  ERBB3 MUTATED                                              0
  ERBB3 WILD-TYPE                                            3
D15V6, multiclass
                                               clus
vv                                              ERBB3 MUTATED ERBB3 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          6             152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       5              17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D15V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED     1  10
  ERBB3 WILD-TYPE  31 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      1   10
  ERBB3 WILD-TYPE   31  152
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO              1              31
  YES            10             152
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB3 MUTATED                                  0     0
  ERBB3 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ERBB3 MUTATED                           1
  ERBB3 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB3 MUTATED                                           0     9
  ERBB3 WILD-TYPE                                         1   129
D15V10, multiclass
                                           clus
vv                                          ERBB3 MUTATED ERBB3 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                                                 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"
D15V11, binary
                 cls
clus                0   1
  ERBB3 MUTATED     2   6
  ERBB3 WILD-TYPE  12 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      2    6
  ERBB3 WILD-TYPE   12  128
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO             6             128
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                 cls
clus               0  1
  ERBB3 MUTATED    7  1
  ERBB3 WILD-TYPE 90 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      7    1
  ERBB3 WILD-TYPE   90   30
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  TUMOR FREE             7              90
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  ERBB3 MUTATED        0      1       1             9       0
  ERBB3 WILD-TYPE      5      9       5           150      14
D15V14, multiclass
               clus
vv              ERBB3 MUTATED ERBB3 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    1               9
  UKRAINE                   1               5
  UNITED STATES             9             150
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  ERBB3 MUTATED    0  7  1  1  2
  ERBB3 WILD-TYPE 14 81 81  0  6
D15V15, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  G1             0              14
  G2             7              81
  G3             1              81
  G4             1               0
  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"
D15V16, continuous
D15V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  ERBB3 MUTATED                                             2
  ERBB3 WILD-TYPE                                          24
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  ERBB3 MUTATED                                        1
  ERBB3 WILD-TYPE                                      7
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  ERBB3 MUTATED                                                 0
  ERBB3 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  ERBB3 MUTATED                1                   6
  ERBB3 WILD-TYPE             36                  87
D15V18, multiclass
                                                 clus
vv                                                ERBB3 MUTATED ERBB3 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 2              24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      1               7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         6              87
[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"
D15V19, continuous
D15V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  ERBB3 MUTATED             1        2             0        0        2
  ERBB3 WILD-TYPE          19       52            12        1        5
D15V21, multiclass
               clus
vv              ERBB3 MUTATED ERBB3 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  2              52
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  2               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"
D15V22, binary
                 cls
clus               0  1
  ERBB3 MUTATED    1  0
  ERBB3 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      1    0
  ERBB3 WILD-TYPE   25    3
                         clus
vv                        ERBB3 MUTATED ERBB3 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  ERBB3 MUTATED                    0                0                   1
  ERBB3 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  ERBB3 MUTATED               2
  ERBB3 WILD-TYPE             2
D15V23, multiclass
                     clus
vv                    ERBB3 MUTATED ERBB3 WILD-TYPE
  DISTANT RECURRENCE              0               2
  LOCAL RECURRENCE                0               2
  PRIMARY TUMOR FIELD             1              19
  REGIONAL SITE                   2               2
[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"
D15V24, binary
                 cls
clus               0  1
  ERBB3 MUTATED    2  1
  ERBB3 WILD-TYPE 14  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      2    1
  ERBB3 WILD-TYPE   14    3
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  CGY             2              14
  GY              1               3
[1] 2 2
[1] FALSE
D15V25, continuous
D15V26, continuous
D15V27, continuous
D15V28, continuous
D15V29, continuous
D15V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ERBB3 MUTATED                                     0
  ERBB3 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ERBB3 MUTATED                                     0                       1
  ERBB3 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ERBB3 MUTATED                         0                       1
  ERBB3 WILD-TYPE                       1                       5
D15V31, multiclass
[1] "Remove cluster labels:" "ERBB3 MUTATED"         
clus
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MP 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE      TCGA-C5-A3HL 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-DG-A2KL 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LI      TCGA-IR-A3LK 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ERBB3 MUTATED                                               0
  ERBB3 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  ERBB3 MUTATED                                                1
  ERBB3 WILD-TYPE                                              9
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  ERBB3 MUTATED                                                                                   6
  ERBB3 WILD-TYPE                                                                                54
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ERBB3 MUTATED                                                                                              3
  ERBB3 WILD-TYPE                                                                                           85
D15V32, multiclass
                                                                                              clus
vv                                                                                             ERBB3 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)                        6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)             3
                                                                                              clus
vv                                                                                             ERBB3 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             9
  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)              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"
D15V33, binary
                 cls
clus               0  1
  ERBB3 MUTATED    5  3
  ERBB3 WILD-TYPE 58 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      5    3
  ERBB3 WILD-TYPE   58   64
         clus
vv        ERBB3 MUTATED ERBB3 WILD-TYPE
  ABSENT              5              58
  PRESENT             3              64
[1] 2 2
[1] FALSE
D15V34, continuous
D15V35, continuous
D15V36, binary
                 cls
clus               0  1
  ERBB3 MUTATED    0  3
  ERBB3 WILD-TYPE 39 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      0    3
  ERBB3 WILD-TYPE   39   83
                                          clus
vv                                         ERBB3 MUTATED ERBB3 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 0              39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             3              83
[1] 2 2
[1] FALSE
D15V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  ERBB3 MUTATED              1           3          0
  ERBB3 WILD-TYPE            7          40         46
D15V38, multiclass
              clus
vv             ERBB3 MUTATED ERBB3 WILD-TYPE
  CURRENT USER             1               7
  FORMER USER              3              40
  NEVER USED               0              46
[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"
D15V39, continuous
D15V40, binary
                 cls
clus               0  1
  ERBB3 MUTATED    8  0
  ERBB3 WILD-TYPE 80 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      8    0
  ERBB3 WILD-TYPE   80   16
         clus
vv        ERBB3 MUTATED ERBB3 WILD-TYPE
  ABSENT              8              80
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  ERBB3 MUTATED             0         1     0
  ERBB3 WILD-TYPE           2        15     1
D15V41, multiclass
[1] "Remove cluster labels:" "ERBB3 MUTATED"         
clus
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
D15V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  ERBB3 MUTATED      0   0    5    0  0   0    1    0   0  0   0  0  2
  ERBB3 WILD-TYPE    1  21   55   22  4   7    5   10  13  1   2  2  7
D15V43, multiclass
      clus
vv     ERBB3 MUTATED ERBB3 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             5              55
  T1B2             0              22
  T2               0               4
  T2A              0               7
  T2A1             1               5
  T2A2             0              10
  T2B              0              13
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               2               7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  ERBB3 MUTATED         1        0         0         0        0         5
  ERBB3 WILD-TYPE       3        1         1         1       28        48
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  ERBB3 MUTATED           3        0         1          1          0         0
  ERBB3 WILD-TYPE        26        4         5          4          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  ERBB3 MUTATED           0          0         0         0
  ERBB3 WILD-TYPE         1         29         2         5
D15V45, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                1               3
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               0              28
  STAGE IB1              5              48
  STAGE IB2              3              26
  STAGE II               0               4
  STAGE IIA              1               5
  STAGE IIA1             1               4
  STAGE IIA2             0               7
  STAGE IIB              0              14
  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(16) Variable = SMAD4 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED     6   1
  SMAD4 WILD-TYPE 144  39
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             183 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1              39 
$`SMAD4 MUTATED`
TCGA-C5-A1M9 TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A3L1 TCGA-IR-A3LA TCGA-Q1-A5R3 
       35.01        31.36        33.30         6.94       137.16        15.95 
TCGA-Q1-A73O 
       14.07 

$`SMAD4 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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-A3QD 
        8.28        39.55        12.36        37.35        30.90        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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-A3LH TCGA-IR-A3LI 
      147.39        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        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-A3Q0 
       20.48        15.58        28.37         8.28        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       30.31         7.99        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.35        13.87        34.62        54.81        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       20.84        15.58        16.41         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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           6.94            0.03 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         137.16          210.67 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          31.36           19.59 
[1] "6.9 - 137.2 (31.4)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.8"
D16V2, continuous
                 vv
clus               T1  T2 T3+T4
  SMAD4 MUTATED     2   2     1
  SMAD4 WILD-TYPE 102  38     4
D16V3, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                2             102
  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"
D16V4, binary
                 cls
clus               0  1
  SMAD4 MUTATED    4  1
  SMAD4 WILD-TYPE 91 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      4    1
  SMAD4 WILD-TYPE   91   43
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             4              91
  1             1              43
[1] 2 2
[1] FALSE
D16V5, binary
                 cls
clus               0  1
  SMAD4 MUTATED    5  0
  SMAD4 WILD-TYPE 74  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      5    0
  SMAD4 WILD-TYPE   74    4
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             5              74
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  SMAD4 MUTATED               0                                5
  SMAD4 WILD-TYPE             4                              153
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  SMAD4 MUTATED                                               0
  SMAD4 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  SMAD4 MUTATED                                     1
  SMAD4 WILD-TYPE                                  21
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  SMAD4 MUTATED                                           1
  SMAD4 WILD-TYPE                                         1
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  SMAD4 MUTATED                                              0
  SMAD4 WILD-TYPE                                            3
D16V6, multiclass
                                               clus
vv                                              SMAD4 MUTATED SMAD4 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          5             153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       1              21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 1               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D16V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED     1   6
  SMAD4 WILD-TYPE  31 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    6
  SMAD4 WILD-TYPE   31  156
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              1              31
  YES             6             156
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD4 MUTATED                                  0     0
  SMAD4 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  SMAD4 MUTATED                           0
  SMAD4 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD4 MUTATED                                           0     6
  SMAD4 WILD-TYPE                                         1   132
D16V10, multiclass
                                           clus
vv                                          SMAD4 MUTATED SMAD4 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                                                 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"
D16V11, binary
                 cls
clus                0   1
  SMAD4 MUTATED     1   5
  SMAD4 WILD-TYPE  13 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    5
  SMAD4 WILD-TYPE   13  129
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             5             129
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                 cls
clus               0  1
  SMAD4 MUTATED    5  1
  SMAD4 WILD-TYPE 92 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      5    1
  SMAD4 WILD-TYPE   92   30
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  TUMOR FREE             5              92
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  SMAD4 MUTATED        0      2       0             5       0
  SMAD4 WILD-TYPE      5      8       6           154      14
D16V14, multiclass
               clus
vv              SMAD4 MUTATED SMAD4 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    2               8
  UKRAINE                   0               6
  UNITED STATES             5             154
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  SMAD4 MUTATED    1  2  3  0  1
  SMAD4 WILD-TYPE 13 86 79  1  7
D16V15, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  G1             1              13
  G2             2              86
  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"
D16V16, continuous
D16V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  SMAD4 MUTATED                                             0
  SMAD4 WILD-TYPE                                          26
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  SMAD4 MUTATED                                        0
  SMAD4 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  SMAD4 MUTATED                                                 0
  SMAD4 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  SMAD4 MUTATED                0                   7
  SMAD4 WILD-TYPE             37                  86
D16V18, multiclass
                                                 clus
vv                                                SMAD4 MUTATED SMAD4 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 0              26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              0              37
  LIFELONG NON-SMOKER                                         7              86
[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"
D16V19, continuous
D16V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  SMAD4 MUTATED             0        4             1        0        0
  SMAD4 WILD-TYPE          20       50            11        1        7
D16V21, multiclass
               clus
vv              SMAD4 MUTATED SMAD4 WILD-TYPE
  COMBINATION               0              20
  EXTERNAL                  4              50
  EXTERNAL BEAM             1              11
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D16V22, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1  0
  SMAD4 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    0
  SMAD4 WILD-TYPE   25    3
                         clus
vv                        SMAD4 MUTATED SMAD4 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  SMAD4 MUTATED                    0                0                   1
  SMAD4 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  SMAD4 MUTATED               0
  SMAD4 WILD-TYPE             4
D16V23, multiclass
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-FU-A23L 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D16V24, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1  0
  SMAD4 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    0
  SMAD4 WILD-TYPE   15    4
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D16V25, continuous
D16V26, continuous
D16V27, continuous
D16V28, continuous
D16V29, continuous
D16V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  SMAD4 MUTATED                                     0
  SMAD4 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  SMAD4 MUTATED                                     0                       1
  SMAD4 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  SMAD4 MUTATED                         0                       0
  SMAD4 WILD-TYPE                       1                       6
D16V31, multiclass
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1              43 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ      TCGA-C5-A1MP 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE      TCGA-C5-A3HL 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-DG-A2KL 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-UC-A7PD      TCGA-WL-A834 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  SMAD4 MUTATED                                               0
  SMAD4 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  SMAD4 MUTATED                                                0
  SMAD4 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  SMAD4 MUTATED                                                                                   3
  SMAD4 WILD-TYPE                                                                                57
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  SMAD4 MUTATED                                                                                              4
  SMAD4 WILD-TYPE                                                                                           84
D16V32, multiclass
                                                                                              clus
vv                                                                                             SMAD4 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                                                                                             SMAD4 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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"
D16V33, binary
                 cls
clus               0  1
  SMAD4 MUTATED    4  2
  SMAD4 WILD-TYPE 59 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      4    2
  SMAD4 WILD-TYPE   59   65
         clus
vv        SMAD4 MUTATED SMAD4 WILD-TYPE
  ABSENT              4              59
  PRESENT             2              65
[1] 2 2
[1] FALSE
D16V34, continuous
D16V35, continuous
D16V36, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1  4
  SMAD4 WILD-TYPE 38 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    4
  SMAD4 WILD-TYPE   38   82
                                          clus
vv                                         SMAD4 MUTATED SMAD4 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 1              38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             4              82
[1] 2 2
[1] FALSE
D16V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  SMAD4 MUTATED              1           2          3
  SMAD4 WILD-TYPE            7          41         43
D16V38, multiclass
              clus
vv             SMAD4 MUTATED SMAD4 WILD-TYPE
  CURRENT USER             1               7
  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"
D16V39, continuous
D16V40, binary
                 cls
clus               0  1
  SMAD4 MUTATED    6  0
  SMAD4 WILD-TYPE 82 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      6    0
  SMAD4 WILD-TYPE   82   16
         clus
vv        SMAD4 MUTATED SMAD4 WILD-TYPE
  ABSENT              6              82
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  SMAD4 MUTATED             0         1     0
  SMAD4 WILD-TYPE           2        15     1
D16V41, multiclass
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1MH 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D16V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  SMAD4 MUTATED      0   1    1    0  0   0    1    1   0  0   1  0  2
  SMAD4 WILD-TYPE    1  20   59   22  4   7    5    9  13  1   1  2  7
D16V43, multiclass
      clus
vv     SMAD4 MUTATED SMAD4 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             1              59
  T1B2             0              22
  T2               0               4
  T2A              0               7
  T2A1             1               5
  T2A2             1               9
  T2B              0              13
  T3               0               1
  T3B              1               1
  T4               0               2
  TX               2               7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  SMAD4 MUTATED         0        0         0         0        1         2
  SMAD4 WILD-TYPE       4        1         1         1       27        51
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  SMAD4 MUTATED           1        1         0          1          0         0
  SMAD4 WILD-TYPE        28        3         6          4          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  SMAD4 MUTATED           0          0         0         0
  SMAD4 WILD-TYPE         1         29         2         5
D16V45, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              2              51
  STAGE IB2              1              28
  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             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(17) Variable = TCTE1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  TCTE1 MUTATED     4   1
  TCTE1 WILD-TYPE 146  39
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              5             185 
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              39 
$`TCTE1 MUTATED`
TCGA-C5-A1MN TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-JX-A3Q0 TCGA-Q1-A73O 
       40.93         6.64         1.18       195.85        14.07 

$`TCTE1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI 
       13.48        12.59        45.96        26.27         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        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-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-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        30.31         7.99        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        13.87        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        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  TCTE1 MUTATED TCTE1 WILD-TYPE 
           1.18            0.03 
  TCTE1 MUTATED TCTE1 WILD-TYPE 
         195.85          210.67 
  TCTE1 MUTATED TCTE1 WILD-TYPE 
          14.07           19.79 
[1] "1.2 - 195.8 (14.1)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.3"
D17V2, continuous
                 vv
clus               T1  T2 T3+T4
  TCTE1 MUTATED     2   0     1
  TCTE1 WILD-TYPE 102  40     4
D17V3, multiclass
       clus
vv      TCTE1 MUTATED TCTE1 WILD-TYPE
  T1                2             102
  T2                0              40
  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"
D17V4, binary
                 cls
clus               0  1
  TCTE1 MUTATED    3  0
  TCTE1 WILD-TYPE 92 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      3    0
  TCTE1 WILD-TYPE   92   44
   clus
vv  TCTE1 MUTATED TCTE1 WILD-TYPE
  0             3              92
  1             0              44
[1] 2 2
[1] FALSE
D17V5, binary
                 cls
clus               0  1
  TCTE1 MUTATED    1  0
  TCTE1 WILD-TYPE 78  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    0
  TCTE1 WILD-TYPE   78    4
   clus
vv  TCTE1 MUTATED TCTE1 WILD-TYPE
  0             1              78
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  TCTE1 MUTATED               0                                5
  TCTE1 WILD-TYPE             4                              153
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  TCTE1 MUTATED                                               0
  TCTE1 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  TCTE1 MUTATED                                     0
  TCTE1 WILD-TYPE                                  22
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  TCTE1 MUTATED                                           0
  TCTE1 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  TCTE1 MUTATED                                              0
  TCTE1 WILD-TYPE                                            3
D17V6, multiclass
                                               clus
vv                                              TCTE1 MUTATED TCTE1 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          5             153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D17V7, binary
                 cls
clus                0   1
  TCTE1 MUTATED     1   4
  TCTE1 WILD-TYPE  31 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    4
  TCTE1 WILD-TYPE   31  158
     clus
vv    TCTE1 MUTATED TCTE1 WILD-TYPE
  NO              1              31
  YES             4             158
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2              55 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCTE1 MUTATED                                  0     0
  TCTE1 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  TCTE1 MUTATED                           1
  TCTE1 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCTE1 MUTATED                                           0     3
  TCTE1 WILD-TYPE                                         1   135
D17V10, multiclass
                                           clus
vv                                          TCTE1 MUTATED TCTE1 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"
D17V11, binary
                 cls
clus                0   1
  TCTE1 MUTATED     1   3
  TCTE1 WILD-TYPE  13 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    3
  TCTE1 WILD-TYPE   13  131
                        clus
vv                       TCTE1 MUTATED TCTE1 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             3             131
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                 cls
clus               0  1
  TCTE1 MUTATED    3  0
  TCTE1 WILD-TYPE 94 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      3    0
  TCTE1 WILD-TYPE   94   31
            clus
vv           TCTE1 MUTATED TCTE1 WILD-TYPE
  TUMOR FREE             3              94
  WITH TUMOR             0              31
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  TCTE1 MUTATED        0      0       0             5       0
  TCTE1 WILD-TYPE      5     10       6           154      14
D17V14, multiclass
               clus
vv              TCTE1 MUTATED TCTE1 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             5             154
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  TCTE1 MUTATED    0  2  2  0  1
  TCTE1 WILD-TYPE 14 86 80  1  7
D17V15, multiclass
    clus
vv   TCTE1 MUTATED TCTE1 WILD-TYPE
  G1             0              14
  G2             2              86
  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"
D17V16, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              28 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-EK-A2RA      TCGA-EX-A69M      TCGA-FU-A2QG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-HM-A3JK      TCGA-HM-A4S6 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-MU-A5YI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-Q1-A6DW      TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V17, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2              55 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  TCTE1 MUTATED                                             1
  TCTE1 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  TCTE1 MUTATED                                        0
  TCTE1 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  TCTE1 MUTATED                                                 0
  TCTE1 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  TCTE1 MUTATED                1                   1
  TCTE1 WILD-TYPE             36                  92
D17V18, multiclass
                                                 clus
vv                                                TCTE1 MUTATED TCTE1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         1              92
[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"
D17V19, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              51 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A2LS      TCGA-C5-A2LT 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DR-A0ZM 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V20, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              81 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1M6      TCGA-C5-A1M8 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A3HD      TCGA-C5-A3HF 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7UE      TCGA-C5-A7UH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DG-A2KM      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VN 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A43B 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A5FO      TCGA-EA-A5O9 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2H0      TCGA-EX-A3L1      TCGA-EX-A449      TCGA-FU-A23L 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A3JK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JX-A5QV      TCGA-LP-A4AU 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A7HU      TCGA-MU-A5YI      TCGA-MY-A5BD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MY-A5BF      TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DW 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-Q1-A73Q      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-WL-A834 
"TCTE1 WILD-TYPE" 
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  TCTE1 MUTATED             1        2             0        0        0
  TCTE1 WILD-TYPE          19       52            12        1        7
D17V21, multiclass
               clus
vv              TCTE1 MUTATED TCTE1 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  2              52
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D17V22, binary
                 cls
clus               0  1
  TCTE1 MUTATED    1  0
  TCTE1 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    0
  TCTE1 WILD-TYPE   25    3
                         clus
vv                        TCTE1 MUTATED TCTE1 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  TCTE1 MUTATED                    0                0                   1
  TCTE1 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  TCTE1 MUTATED               0
  TCTE1 WILD-TYPE             4
D17V23, multiclass
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V24, binary
                 cls
clus               0  1
  TCTE1 MUTATED    1  0
  TCTE1 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    0
  TCTE1 WILD-TYPE   15    4
     clus
vv    TCTE1 MUTATED TCTE1 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D17V25, continuous
D17V26, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2              99 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MP      TCGA-C5-A1MQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EX-A449      TCGA-FU-A2QG      TCGA-FU-A3EO 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A770 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V27, continuous
D17V28, continuous
D17V29, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2             107 
     TCGA-BI-A0VS      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MP      TCGA-C5-A1MQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EA-A6QX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EX-A1H6      TCGA-EX-A449      TCGA-FU-A2QG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-LP-A5U2      TCGA-MU-A51Y 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V30, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2             101 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MP      TCGA-C5-A1MQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A5XV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-IR-A3L7 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q8 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-Q1-A73Q      TCGA-RA-A741      TCGA-UC-A7PD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-UC-A7PF 
"TCTE1 WILD-TYPE" 
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  TCTE1 MUTATED                                     0
  TCTE1 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  TCTE1 MUTATED                                     0                       0
  TCTE1 WILD-TYPE                                   7                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  TCTE1 MUTATED                         0                       0
  TCTE1 WILD-TYPE                       1                       6
D17V31, multiclass
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  TCTE1 MUTATED                                               0
  TCTE1 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  TCTE1 MUTATED                                                0
  TCTE1 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  TCTE1 MUTATED                                                                                   1
  TCTE1 WILD-TYPE                                                                                59
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  TCTE1 MUTATED                                                                                              2
  TCTE1 WILD-TYPE                                                                                           86
D17V32, multiclass
                                                                                              clus
vv                                                                                             TCTE1 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                                                                                             TCTE1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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"
D17V33, binary
                 cls
clus               0  1
  TCTE1 MUTATED    1  1
  TCTE1 WILD-TYPE 62 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    1
  TCTE1 WILD-TYPE   62   66
         clus
vv        TCTE1 MUTATED TCTE1 WILD-TYPE
  ABSENT              1              62
  PRESENT             1              66
[1] 2 2
[1] FALSE
D17V34, continuous
D17V35, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2             138 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A5FO      TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2GZ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2PK      TCGA-EK-A2R7      TCGA-EK-A2R8      TCGA-EK-A2R9 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EK-A2RC      TCGA-EK-A2RD      TCGA-EK-A2RE 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2RK      TCGA-EK-A2RL      TCGA-EK-A2RM      TCGA-EK-A2RN 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-EK-A3GJ      TCGA-EK-A3GK      TCGA-EX-A1H5 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L      TCGA-EX-A69M 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG      TCGA-FU-A3EO 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI      TCGA-FU-A3TQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A40J 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770      TCGA-HG-A2PA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX      TCGA-LP-A5U2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-MU-A5YI      TCGA-MY-A5BD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV      TCGA-Q1-A73P 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-UC-A7PD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-UC-A7PF      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V36, binary
                 cls
clus               0  1
  TCTE1 MUTATED    2  3
  TCTE1 WILD-TYPE 37 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      2    3
  TCTE1 WILD-TYPE   37   83
                                          clus
vv                                         TCTE1 MUTATED TCTE1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 2              37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             3              83
[1] 2 2
[1] FALSE
D17V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  TCTE1 MUTATED              0           1          1
  TCTE1 WILD-TYPE            8          42         45
D17V38, multiclass
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              2              95 
     TCGA-C5-A1BI      TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M6 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7UH      TCGA-C5-A7X3 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DG-A2KM      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5O9 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EA-A5ZE      TCGA-EA-A5ZF      TCGA-EK-A2R7      TCGA-EK-A3GK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-LP-A5U2      TCGA-LP-A5U3      TCGA-LP-A7HU      TCGA-Q1-A5R1 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DV      TCGA-Q1-A73P 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-UC-A7PD      TCGA-WL-A834 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V39, continuous
D17V40, binary
                 cls
clus               0  1
  TCTE1 MUTATED    1  0
  TCTE1 WILD-TYPE 87 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCTE1 MUTATED      1    0
  TCTE1 WILD-TYPE   87   16
         clus
vv        TCTE1 MUTATED TCTE1 WILD-TYPE
  ABSENT              1              87
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  TCTE1 MUTATED             0         1     0
  TCTE1 WILD-TYPE           2        15     1
D17V41, multiclass
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MQ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
D17V42, continuous
[1] "Remove cluster labels:" "TCTE1 MUTATED"         
clus
  TCTE1 MUTATED TCTE1 WILD-TYPE 
              1               9 
     TCGA-C5-A1BN      TCGA-C5-A1MH      TCGA-C5-A1ML      TCGA-C5-A1MP 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-HM-A3JK      TCGA-JW-A852      TCGA-JX-A3Q8 
"TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" "TCTE1 WILD-TYPE" 
     TCGA-MU-A51Y 
"TCTE1 WILD-TYPE" 
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  TCTE1 MUTATED      0   0    1    1  0   0    0    0   0  1   0  0  1
  TCTE1 WILD-TYPE    1  21   59   21  4   7    6   10  13  0   2  2  8
D17V43, multiclass
      clus
vv     TCTE1 MUTATED TCTE1 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             1              59
  T1B2             1              21
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              0              13
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               1               8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  TCTE1 MUTATED         0        0         0         0        0         1
  TCTE1 WILD-TYPE       4        1         1         1       28        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  TCTE1 MUTATED           2        0         0          0          0         0
  TCTE1 WILD-TYPE        27        4         6          5          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  TCTE1 MUTATED           1          1         0         0
  TCTE1 WILD-TYPE         0         28         2         5
D17V45, multiclass
            clus
vv           TCTE1 MUTATED TCTE1 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              2              27
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              0              14
  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(18) Variable = NHS MUTATION ANALYSIS
D18V1, survival
               sevent
clus2             0   1
  NHS MUTATED    11   1
  NHS WILD-TYPE 139  39
  NHS MUTATED NHS WILD-TYPE 
           12           178 
  NHS MUTATED NHS WILD-TYPE 
            1            39 
$`NHS MUTATED`
TCGA-C5-A1BQ TCGA-DG-A2KK TCGA-DS-A5RQ TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2PG 
       19.86        50.76        16.83        14.50        26.01         1.51 
TCGA-EK-A2R8 TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JW-A5VL TCGA-LP-A5U3 TCGA-MU-A5YI 
        1.45       137.16        78.71        15.58         0.82        34.62 

$`NHS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
      131.11         9.34         1.12        58.88        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       28.90        22.98        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 
       12.36        37.35        30.90        31.36        33.30        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA 
       25.02        14.50        26.40        24.56        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
        6.64        19.27         0.43         0.59         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       24.56        21.44        20.48        28.37         8.28        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      195.85        30.31         7.99        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.30        13.35        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
        3.88        11.67        93.99        26.01 

  NHS MUTATED NHS WILD-TYPE 
         0.82          0.03 
  NHS MUTATED NHS WILD-TYPE 
       137.16        210.67 
  NHS MUTATED NHS WILD-TYPE 
       18.345        19.690 
[1] "0.8 - 137.2 (18.3)" "0.0 - 210.7 (19.7)"
[1] "hr=" "2.6"
D18V2, continuous
               vv
clus            T1 T2 T3+T4
  NHS MUTATED    8  2     0
  NHS WILD-TYPE 96 38     5
D18V3, multiclass
       clus
vv      NHS MUTATED NHS WILD-TYPE
  T1              8            96
  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"
D18V4, binary
               cls
clus             0  1
  NHS MUTATED    6  2
  NHS WILD-TYPE 89 42
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      6    2
  NHS WILD-TYPE   89   42
   clus
vv  NHS MUTATED NHS WILD-TYPE
  0           6            89
  1           2            42
[1] 2 2
[1] FALSE
D18V5, binary
               cls
clus             0  1
  NHS MUTATED    6  0
  NHS WILD-TYPE 73  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      6    0
  NHS WILD-TYPE   73    4
   clus
vv  NHS MUTATED NHS WILD-TYPE
  0           6            73
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  NHS MUTATED               0                               11
  NHS WILD-TYPE             4                              147
               vv
clus            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  NHS MUTATED                                               0
  NHS WILD-TYPE                                             5
               vv
clus            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  NHS MUTATED                                     0
  NHS WILD-TYPE                                  22
               vv
clus            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  NHS MUTATED                                           1
  NHS WILD-TYPE                                         1
               vv
clus            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  NHS MUTATED                                              0
  NHS WILD-TYPE                                            3
D18V6, multiclass
                                               clus
vv                                              NHS MUTATED NHS WILD-TYPE
  ADENOSQUAMOUS                                           0             4
  CERVICAL SQUAMOUS CELL CARCINOMA                       11           147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE           0             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                     0            22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX               1             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE            0             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"
D18V7, binary
               cls
clus              0   1
  NHS MUTATED     0  12
  NHS WILD-TYPE  32 150
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      0   12
  NHS WILD-TYPE   32  150
     clus
vv    NHS MUTATED NHS WILD-TYPE
  NO            0            32
  YES          12           150
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NHS MUTATED                                  1     2
  NHS WILD-TYPE                                7    17
               vv
clus            BLACK OR AFRICAN AMERICAN
  NHS MUTATED                           3
  NHS WILD-TYPE                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NHS MUTATED                                           0     5
  NHS WILD-TYPE                                         1   133
D18V10, multiclass
                                           clus
vv                                          NHS MUTATED NHS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    1             7
  ASIAN                                               2            17
  BLACK OR AFRICAN AMERICAN                           3            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           133
[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
  NHS MUTATED     1   7
  NHS WILD-TYPE  13 127
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      1    7
  NHS WILD-TYPE   13  127
                        clus
vv                       NHS MUTATED NHS WILD-TYPE
  HISPANIC OR LATINO               1            13
  NOT HISPANIC OR LATINO           7           127
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
               cls
clus             0  1
  NHS MUTATED    8  1
  NHS WILD-TYPE 89 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      8    1
  NHS WILD-TYPE   89   30
            clus
vv           NHS MUTATED NHS WILD-TYPE
  TUMOR FREE           8            89
  WITH TUMOR           1            30
[1] 2 2
[1] FALSE
               vv
clus            CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  NHS MUTATED        1      0       1             8       2
  NHS WILD-TYPE      4     10       5           151      12
D18V14, multiclass
               clus
vv              NHS MUTATED NHS WILD-TYPE
  CANADA                  1             4
  RUSSIA                  0            10
  UKRAINE                 1             5
  UNITED STATES           8           151
  VIETNAM                 2            12
[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            G1 G2 G3 G4 GX
  NHS MUTATED    1  4  6  1  0
  NHS WILD-TYPE 13 84 76  0  8
D18V15, multiclass
    clus
vv   NHS MUTATED NHS WILD-TYPE
  G1           1            13
  G2           4            84
  G3           6            76
  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"
D18V16, continuous
D18V17, continuous
               vv
clus            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  NHS MUTATED                                             3
  NHS WILD-TYPE                                          23
               vv
clus            CURRENT REFORMED SMOKER FOR > 15 YEARS
  NHS MUTATED                                        1
  NHS WILD-TYPE                                      7
               vv
clus            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  NHS MUTATED                                                 0              1
  NHS WILD-TYPE                                               1             36
               vv
clus            LIFELONG NON-SMOKER
  NHS MUTATED                     5
  NHS WILD-TYPE                  88
D18V18, multiclass
                                                 clus
vv                                                NHS MUTATED NHS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS               3            23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                    1             7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED           0             1
  CURRENT SMOKER                                            1            36
  LIFELONG NON-SMOKER                                       5            88
[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"
D18V19, continuous
D18V20, continuous
               vv
clus            COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  NHS MUTATED             0        7             0        0        0
  NHS WILD-TYPE          20       47            12        1        7
D18V21, multiclass
               clus
vv              NHS MUTATED NHS WILD-TYPE
  COMBINATION             0            20
  EXTERNAL                7            47
  EXTERNAL BEAM           0            12
  IMPLANTS                0             1
  INTERNAL                0             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"
D18V22, binary
               cls
clus             0  1
  NHS MUTATED    0  0
  NHS WILD-TYPE 26  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      0    0
  NHS WILD-TYPE   26    3
               vv
clus            DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  NHS MUTATED                    0                0                   3
  NHS WILD-TYPE                  2                2                  17
               vv
clus            REGIONAL SITE
  NHS MUTATED               0
  NHS WILD-TYPE             4
D18V23, multiclass
                     clus
vv                    NHS MUTATED NHS WILD-TYPE
  DISTANT RECURRENCE            0             2
  LOCAL RECURRENCE              0             2
  PRIMARY TUMOR FIELD           3            17
  REGIONAL SITE                 0             4
[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"
D18V24, binary
               cls
clus             0  1
  NHS MUTATED    1  1
  NHS WILD-TYPE 15  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      1    1
  NHS WILD-TYPE   15    3
     clus
vv    NHS MUTATED NHS WILD-TYPE
  CGY           1            15
  GY            1             3
[1] 2 2
[1] FALSE
D18V25, continuous
D18V26, continuous
D18V27, continuous
D18V28, continuous
D18V29, continuous
D18V30, continuous
               vv
clus            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  NHS MUTATED                                     0
  NHS WILD-TYPE                                   2
               vv
clus            MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  NHS MUTATED                                     0                       0
  NHS WILD-TYPE                                   7                      28
               vv
clus            POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  NHS MUTATED                         0                       1
  NHS WILD-TYPE                       1                       5
D18V31, multiclass
[1] "Remove cluster labels:" "NHS MUTATED"           
clus
  NHS MUTATED NHS WILD-TYPE 
            1            43 
   TCGA-BI-A20A    TCGA-C5-A0TN    TCGA-C5-A1BE    TCGA-C5-A1BK    TCGA-C5-A1BM 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-C5-A1M5    TCGA-C5-A1M7    TCGA-C5-A1M8    TCGA-C5-A1M9    TCGA-C5-A1ME 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-C5-A1MF    TCGA-C5-A1MJ    TCGA-C5-A1MP    TCGA-C5-A1MQ    TCGA-C5-A2LS 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2M1    TCGA-C5-A3HE 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-C5-A3HL    TCGA-C5-A7CG    TCGA-C5-A7CJ    TCGA-C5-A7UC    TCGA-DG-A2KL 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-DR-A0ZM    TCGA-DS-A0VK    TCGA-DS-A0VL    TCGA-DS-A0VM    TCGA-DS-A0VN 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-DS-A1OA    TCGA-DS-A3LQ    TCGA-EA-A50E    TCGA-EK-A2RN    TCGA-EK-A2RO 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-EX-A1H5    TCGA-EX-A449    TCGA-FU-A3EO    TCGA-HM-A4S6    TCGA-IR-A3LI 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
   TCGA-IR-A3LK    TCGA-UC-A7PD    TCGA-WL-A834 
"NHS WILD-TYPE" "NHS WILD-TYPE" "NHS WILD-TYPE" 
               vv
clus            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  NHS MUTATED                                               0
  NHS WILD-TYPE                                             2
               vv
clus            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  NHS MUTATED                                                0
  NHS WILD-TYPE                                             10
               vv
clus            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  NHS MUTATED                                                                                   6
  NHS WILD-TYPE                                                                                54
               vv
clus            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  NHS MUTATED                                                                                              6
  NHS WILD-TYPE                                                                                           82
D18V32, multiclass
                                                                                              clus
vv                                                                                             NHS 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)           6
                                                                                              clus
vv                                                                                             NHS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            2
  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)            82
[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"
D18V33, binary
               cls
clus             0  1
  NHS MUTATED    3  5
  NHS WILD-TYPE 60 62
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      3    5
  NHS WILD-TYPE   60   62
         clus
vv        NHS MUTATED NHS WILD-TYPE
  ABSENT            3            60
  PRESENT           5            62
[1] 2 2
[1] FALSE
D18V34, continuous
D18V35, continuous
D18V36, binary
               cls
clus             0  1
  NHS MUTATED    4  4
  NHS WILD-TYPE 35 82
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      4    4
  NHS WILD-TYPE   35   82
                                          clus
vv                                         NHS MUTATED NHS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA               4            35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA           4            82
[1] 2 2
[1] FALSE
D18V37, continuous
               vv
clus            CURRENT USER FORMER USER NEVER USED
  NHS MUTATED              0           1          3
  NHS WILD-TYPE            8          42         43
D18V38, multiclass
              clus
vv             NHS MUTATED NHS WILD-TYPE
  CURRENT USER           0             8
  FORMER USER            1            42
  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"
D18V39, continuous
D18V40, binary
               cls
clus             0  1
  NHS MUTATED    6  1
  NHS WILD-TYPE 82 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      6    1
  NHS WILD-TYPE   82   15
         clus
vv        NHS MUTATED NHS WILD-TYPE
  ABSENT            6            82
  PRESENT           1            15
[1] 2 2
[1] FALSE
               vv
clus            CARBOPLATIN CISPLATIN OTHER
  NHS MUTATED             0         0     0
  NHS WILD-TYPE           2        16     1
D18V41, multiclass
D18V42, continuous
               vv
clus            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  NHS MUTATED      1   0    5    2  0   0    2    0   0  0   0  0  0
  NHS WILD-TYPE    0  21   55   20  4   7    4   10  13  1   2  2  9
D18V43, multiclass
      clus
vv     NHS MUTATED NHS WILD-TYPE
  T1A1           1             0
  T1B            0            21
  T1B1           5            55
  T1B2           2            20
  T2             0             4
  T2A            0             7
  T2A1           2             4
  T2A2           0            10
  T2B            0            13
  T3             0             1
  T3B            0             2
  T4             0             2
  TX             0             9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V44, continuous
               vv
clus            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  NHS MUTATED         0        0         1         0        0         4
  NHS WILD-TYPE       4        1         0         1       28        49
               vv
clus            STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  NHS MUTATED           2        0         0          2          0         0
  NHS WILD-TYPE        27        4         6          3          7        14
               vv
clus            STAGE III STAGE IIIB STAGE IVA STAGE IVB
  NHS MUTATED           0          2         0         0
  NHS WILD-TYPE         1         27         2         5
D18V45, multiclass
            clus
vv           NHS MUTATED NHS WILD-TYPE
  STAGE I              0             4
  STAGE IA             0             1
  STAGE IA1            1             0
  STAGE IA2            0             1
  STAGE IB             0            28
  STAGE IB1            4            49
  STAGE IB2            2            27
  STAGE II             0             4
  STAGE IIA            0             6
  STAGE IIA1           2             3
  STAGE IIA2           0             7
  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(19) Variable = LIN9 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  LIN9 MUTATED     6   1
  LIN9 WILD-TYPE 144  39
  LIN9 MUTATED LIN9 WILD-TYPE 
             7            183 
  LIN9 MUTATED LIN9 WILD-TYPE 
             1             39 
$`LIN9 MUTATED`
TCGA-C5-A1MF TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A5ZF TCGA-EK-A2R9 
       53.16        31.36        33.30        13.05        14.96         0.13 
TCGA-IR-A3LK 
       29.85 

$`LIN9 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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-A3QE 
        8.28        39.55        12.36        37.35        30.90        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.99        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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-A3LL 
       66.81       117.40        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-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       195.85        30.31         7.99 
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 
       13.87        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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  LIN9 MUTATED LIN9 WILD-TYPE 
          0.13           0.03 
  LIN9 MUTATED LIN9 WILD-TYPE 
         53.16         210.67 
  LIN9 MUTATED LIN9 WILD-TYPE 
         29.85          19.59 
[1] "0.1 - 53.2 (29.9)"  "0.0 - 210.7 (19.6)"
[1] "hr=" "1.2"
D19V2, continuous
                vv
clus             T1 T2 T3+T4
  LIN9 MUTATED    6  1     0
  LIN9 WILD-TYPE 98 39     5
D19V3, multiclass
       clus
vv      LIN9 MUTATED LIN9 WILD-TYPE
  T1               6             98
  T2               1             39
  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
  LIN9 MUTATED    5  1
  LIN9 WILD-TYPE 90 43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      5    1
  LIN9 WILD-TYPE   90   43
   clus
vv  LIN9 MUTATED LIN9 WILD-TYPE
  0            5             90
  1            1             43
[1] 2 2
[1] FALSE
D19V5, binary
                cls
clus              0  1
  LIN9 MUTATED    5  0
  LIN9 WILD-TYPE 74  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      5    0
  LIN9 WILD-TYPE   74    4
   clus
vv  LIN9 MUTATED LIN9 WILD-TYPE
  0            5             74
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  LIN9 MUTATED               0                                7
  LIN9 WILD-TYPE             4                              151
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  LIN9 MUTATED                                               0
  LIN9 WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  LIN9 MUTATED                                     0
  LIN9 WILD-TYPE                                  22
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  LIN9 MUTATED                                           0
  LIN9 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  LIN9 MUTATED                                              0
  LIN9 WILD-TYPE                                            3
D19V6, multiclass
                                               clus
vv                                              LIN9 MUTATED LIN9 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         7            151
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D19V7, binary
                cls
clus               0   1
  LIN9 MUTATED     1   6
  LIN9 WILD-TYPE  31 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      1    6
  LIN9 WILD-TYPE   31  156
     clus
vv    LIN9 MUTATED LIN9 WILD-TYPE
  NO             1             31
  YES            6            156
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "LIN9 MUTATED"          
clus
  LIN9 MUTATED LIN9 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
D19V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIN9 MUTATED                                  0     1
  LIN9 WILD-TYPE                                8    18
                vv
clus             BLACK OR AFRICAN AMERICAN
  LIN9 MUTATED                           0
  LIN9 WILD-TYPE                        16
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIN9 MUTATED                                           0     6
  LIN9 WILD-TYPE                                         1   132
D19V10, multiclass
                                           clus
vv                                          LIN9 MUTATED LIN9 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"
D19V11, binary
                cls
clus               0   1
  LIN9 MUTATED     0   6
  LIN9 WILD-TYPE  14 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      0    6
  LIN9 WILD-TYPE   14  128
                        clus
vv                       LIN9 MUTATED LIN9 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            6            128
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                cls
clus              0  1
  LIN9 MUTATED    4  2
  LIN9 WILD-TYPE 93 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      4    2
  LIN9 WILD-TYPE   93   29
            clus
vv           LIN9 MUTATED LIN9 WILD-TYPE
  TUMOR FREE            4             93
  WITH TUMOR            2             29
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  LIN9 MUTATED        0      2       0             4       1
  LIN9 WILD-TYPE      5      8       6           155      13
D19V14, multiclass
               clus
vv              LIN9 MUTATED LIN9 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   2              8
  UKRAINE                  0              6
  UNITED STATES            4            155
  VIETNAM                  1             13
[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             G1 G2 G3 G4 GX
  LIN9 MUTATED    1  3  3  0  0
  LIN9 WILD-TYPE 13 85 79  1  8
D19V15, multiclass
    clus
vv   LIN9 MUTATED LIN9 WILD-TYPE
  G1            1             13
  G2            3             85
  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"
D19V16, continuous
[1] "Remove cluster labels:" "LIN9 MUTATED"          
clus
  LIN9 MUTATED LIN9 WILD-TYPE 
             1             28 
    TCGA-BI-A0VR     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1BQ 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DS-A3LQ 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3TX 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JX-A3Q0     TCGA-MU-A5YI 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
D19V17, continuous
[1] "Remove cluster labels:" "LIN9 MUTATED"          
clus
  LIN9 MUTATED LIN9 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  LIN9 MUTATED                                             1
  LIN9 WILD-TYPE                                          25
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  LIN9 MUTATED                                        0
  LIN9 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  LIN9 MUTATED                                                 0              0
  LIN9 WILD-TYPE                                               1             37
                vv
clus             LIFELONG NON-SMOKER
  LIN9 MUTATED                     5
  LIN9 WILD-TYPE                  88
D19V18, multiclass
                                                 clus
vv                                                LIN9 MUTATED LIN9 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                1             25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             0             37
  LIFELONG NON-SMOKER                                        5             88
[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"
D19V19, continuous
[1] "Remove cluster labels:" "LIN9 MUTATED"          
clus
  LIN9 MUTATED LIN9 WILD-TYPE 
             1             51 
    TCGA-BI-A0VR     TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7     TCGA-C5-A1ME 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CL     TCGA-C5-A7CO 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DR-A0ZM     TCGA-DS-A5RQ 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EK-A2RA     TCGA-EX-A1H5     TCGA-FU-A2QG 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ     TCGA-FU-A3TX 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
D19V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  LIN9 MUTATED             1        2             0        0        0
  LIN9 WILD-TYPE          19       52            12        1        7
D19V21, multiclass
               clus
vv              LIN9 MUTATED LIN9 WILD-TYPE
  COMBINATION              1             19
  EXTERNAL                 2             52
  EXTERNAL BEAM            0             12
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D19V22, binary
                cls
clus              0  1
  LIN9 MUTATED    1  0
  LIN9 WILD-TYPE 25  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      1    0
  LIN9 WILD-TYPE   25    3
                         clus
vv                        LIN9 MUTATED LIN9 WILD-TYPE
  COMPLETED AS PLANNED               1             25
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  LIN9 MUTATED                    0                0                   0
  LIN9 WILD-TYPE                  2                2                  20
                vv
clus             REGIONAL SITE
  LIN9 MUTATED               0
  LIN9 WILD-TYPE             4
D19V23, multiclass
D19V24, binary
                cls
clus              0  1
  LIN9 MUTATED    0  0
  LIN9 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      0    0
  LIN9 WILD-TYPE   16    4
D19V25, continuous
D19V26, continuous
D19V27, continuous
D19V28, continuous
D19V29, continuous
D19V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  LIN9 MUTATED                                     0
  LIN9 WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  LIN9 MUTATED                                     1                       1
  LIN9 WILD-TYPE                                   6                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  LIN9 MUTATED                         0                       0
  LIN9 WILD-TYPE                       1                       6
D19V31, multiclass
[1] "Remove cluster labels:" "LIN9 MUTATED"          
clus
  LIN9 MUTATED LIN9 WILD-TYPE 
             2             42 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BK 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MJ     TCGA-C5-A1MP 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2M1     TCGA-C5-A3HE     TCGA-C5-A3HL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-DG-A2KL 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EA-A50E 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EX-A1H5     TCGA-EX-A449 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-HM-A4S6     TCGA-IR-A3LH     TCGA-IR-A3LI 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"LIN9 WILD-TYPE" "LIN9 WILD-TYPE" 
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  LIN9 MUTATED                                               0
  LIN9 WILD-TYPE                                             2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  LIN9 MUTATED                                                1
  LIN9 WILD-TYPE                                              9
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  LIN9 MUTATED                                                                                   3
  LIN9 WILD-TYPE                                                                                57
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  LIN9 MUTATED                                                                                              2
  LIN9 WILD-TYPE                                                                                           86
D19V32, multiclass
                                                                                              clus
vv                                                                                             LIN9 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)                       3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            2
                                                                                              clus
vv                                                                                             LIN9 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            9
  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"
D19V33, binary
                cls
clus              0  1
  LIN9 MUTATED    3  3
  LIN9 WILD-TYPE 60 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      3    3
  LIN9 WILD-TYPE   60   64
         clus
vv        LIN9 MUTATED LIN9 WILD-TYPE
  ABSENT             3             60
  PRESENT            3             64
[1] 2 2
[1] FALSE
D19V34, continuous
D19V35, continuous
D19V36, binary
                cls
clus              0  1
  LIN9 MUTATED    2  3
  LIN9 WILD-TYPE 37 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      2    3
  LIN9 WILD-TYPE   37   83
                                          clus
vv                                         LIN9 MUTATED LIN9 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                2             37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            3             83
[1] 2 2
[1] FALSE
D19V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  LIN9 MUTATED              0           3          3
  LIN9 WILD-TYPE            8          40         43
D19V38, multiclass
              clus
vv             LIN9 MUTATED LIN9 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"
D19V39, continuous
D19V40, binary
                cls
clus              0  1
  LIN9 MUTATED    6  0
  LIN9 WILD-TYPE 82 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIN9 MUTATED      6    0
  LIN9 WILD-TYPE   82   16
         clus
vv        LIN9 MUTATED LIN9 WILD-TYPE
  ABSENT             6             82
  PRESENT            0             16
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  LIN9 MUTATED             0         0     0
  LIN9 WILD-TYPE           2        16     1
D19V41, multiclass
D19V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  LIN9 MUTATED      0   1    3    2  0   0    0    1   0  0   0  0  0
  LIN9 WILD-TYPE    1  20   57   20  4   7    6    9  13  1   2  2  9
D19V43, multiclass
      clus
vv     LIN9 MUTATED LIN9 WILD-TYPE
  T1A1            0              1
  T1B             1             20
  T1B1            3             57
  T1B2            2             20
  T2              0              4
  T2A             0              7
  T2A1            0              6
  T2A2            1              9
  T2B             0             13
  T3              0              1
  T3B             0              2
  T4              0              2
  TX              0              9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  LIN9 MUTATED         0        0         0         0        1         2
  LIN9 WILD-TYPE       4        1         1         1       27        51
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  LIN9 MUTATED           2        1         0          0          0         0
  LIN9 WILD-TYPE        27        3         6          5          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  LIN9 MUTATED           0          1         0         0
  LIN9 WILD-TYPE         1         28         2         5
D19V45, multiclass
            clus
vv           LIN9 MUTATED LIN9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              1             27
  STAGE IB1             2             51
  STAGE IB2             2             27
  STAGE II              1              3
  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 = C12ORF43 MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     4   0
  C12ORF43 WILD-TYPE 146  40
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 4                186 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 0                 40 
$`C12ORF43 MUTATED`
TCGA-BI-A20A TCGA-DR-A0ZM TCGA-EK-A2H0 TCGA-JX-A3Q0 
       23.67        58.88        45.96       195.85 

$`C12ORF43 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        87.75        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       12.59        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        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-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-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        30.31         7.99        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        13.87        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        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             23.67               0.03 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
            195.85             210.67 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
            52.420             19.315 
[1] "23.7 - 195.8 (52.4)" "0.0 - 210.7 (19.3)" 
[1] "hr="     "2.6e+07"
D20V2, continuous
                    vv
clus                  T1  T2 T3+T4
  C12ORF43 MUTATED     1   1     1
  C12ORF43 WILD-TYPE 103  39     4
D20V3, 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"
D20V4, 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
D20V5, 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
                    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                                  22
                    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                                            3
D20V6, 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                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   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"
D20V7, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     2   2
  C12ORF43 WILD-TYPE  30 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      2    2
  C12ORF43 WILD-TYPE   30  160
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 2                 30
  YES                2                160
[1] 2 2
[1] FALSE
D20V8, 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" 
D20V9, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                119 
        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-A3Y4 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A43B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5FO         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EK-A2RA         TCGA-EK-A2RO 
"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-EX-A69M 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         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-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"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
D20V10, 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"
D20V11, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   3
  C12ORF43 WILD-TYPE  14 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    3
  C12ORF43 WILD-TYPE   14  131
                        clus
vv                       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO                3                131
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    4  0
  C12ORF43 WILD-TYPE 93 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      4    0
  C12ORF43 WILD-TYPE   93   31
            clus
vv           C12ORF43 MUTATED C12ORF43 WILD-TYPE
  TUMOR FREE                4                 93
  WITH TUMOR                0                 31
[1] 2 2
[1] FALSE
                    vv
clus                 CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  C12ORF43 MUTATED        0      0       0             4       0
  C12ORF43 WILD-TYPE      5     10       6           155      14
D20V14, multiclass
               clus
vv              C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CANADA                       0                  5
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                4                155
  VIETNAM                      0                 14
[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                 G1 G2 G3 G4 GX
  C12ORF43 MUTATED    0  2  2  0  0
  C12ORF43 WILD-TYPE 14 86 80  1  8
D20V15, 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"
D20V16, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                 28 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A2M2         TCGA-C5-A3HD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-DG-A2KK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EK-A2RA         TCGA-EX-A69M 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         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" 
D20V17, 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" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  C12ORF43 MUTATED                                             1
  C12ORF43 WILD-TYPE                                          25
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  C12ORF43 MUTATED                                        0
  C12ORF43 WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  C12ORF43 MUTATED                                                 0
  C12ORF43 WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  C12ORF43 MUTATED                1                   0
  C12ORF43 WILD-TYPE             36                  93
D20V18, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                163 
        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-A1BI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BK         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M5         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-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         TCGA-C5-A1ML 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MN         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-A2LZ 
"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-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         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-A2KH         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-A439         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-A5ZD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZE         TCGA-EA-A5ZF         TCGA-EA-A6QX 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A78R         TCGA-EK-A2RA         TCGA-EK-A2RB 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A3GM         TCGA-EX-A1H5         TCGA-EX-A1H6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-EX-A69L         TCGA-EX-A69M 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         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-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"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" 
D20V19, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 50 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CL         TCGA-C5-A7CO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-DG-A2KK         TCGA-DS-A5RQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         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-A3TX         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" 
D20V20, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 80 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M8         TCGA-C5-A1M9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MQ         TCGA-C5-A2LT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CM         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-A2KL         TCGA-DG-A2KM         TCGA-DS-A0VK 
"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-A7WH         TCGA-DS-A7WI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3Y4         TCGA-EA-A43B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A5FO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A3L1         TCGA-EX-A449 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A3JJ         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-JX-A5QV         TCGA-LP-A4AU 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-LP-A4AX         TCGA-LP-A7HU         TCGA-MU-A5YI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-MY-A5BD         TCGA-MY-A5BF         TCGA-Q1-A5R2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-Q1-A6DW         TCGA-Q1-A73O 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-R2-A69V 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-RA-A741         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  C12ORF43 MUTATED             0        1             2        0        0
  C12ORF43 WILD-TYPE          20       53            10        1        7
D20V21, multiclass
               clus
vv              C12ORF43 MUTATED C12ORF43 WILD-TYPE
  COMBINATION                  0                 20
  EXTERNAL                     1                 53
  EXTERNAL BEAM                2                 10
  IMPLANTS                     0                  1
  INTERNAL                     0                  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"
D20V22, 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
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  C12ORF43 MUTATED                    0                0                   1
  C12ORF43 WILD-TYPE                  2                2                  19
                    vv
clus                 REGIONAL SITE
  C12ORF43 MUTATED               0
  C12ORF43 WILD-TYPE             4
D20V23, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                 27 
        TCGA-C5-A0TN         TCGA-C5-A1BF         TCGA-C5-A1BQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CM         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-DS-A7WF         TCGA-EA-A43B         TCGA-EA-A5FO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23L         TCGA-FU-A3HY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-HM-A3JJ         TCGA-HM-A4S6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-JW-A5VG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-R2-A69V         TCGA-WL-A834 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D20V24, binary
                    cls
clus                  0  1
  C12ORF43 MUTATED    1  0
  C12ORF43 WILD-TYPE 15  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    0
  C12ORF43 WILD-TYPE   15    4
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  CGY                1                 15
  GY                 0                  4
[1] 2 2
[1] FALSE
D20V25, continuous
D20V26, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                100 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"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-A1MH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LS         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-A2LZ         TCGA-C5-A2M1         TCGA-C5-A2M2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HE         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"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-A2KL         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-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-A3HT         TCGA-EA-A3HU         TCGA-EA-A3QD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A449         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" 
D20V27, 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" 
D20V28, continuous
D20V29, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                108 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"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-A1MH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LS         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-A2LZ         TCGA-C5-A2M1         TCGA-C5-A2M2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HE         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"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-A2KL         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-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-A44S 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A556         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EK-A2RN         TCGA-EX-A1H6 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A449         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" 
D20V30, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 1                102 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"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-A1MH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LS         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-A2LZ         TCGA-C5-A2M1         TCGA-C5-A2M2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HE         TCGA-C5-A3HF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"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-A2KL         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-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-A3HT         TCGA-EA-A3HU         TCGA-EA-A3QD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A69M         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                                   2
                    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                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  C12ORF43 MUTATED                         0
  C12ORF43 WILD-TYPE                       6
D20V31, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 42 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BK 
"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-A1MJ         TCGA-C5-A1MP 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MQ         TCGA-C5-A2LS         TCGA-C5-A2LT 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2M1 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HL         TCGA-C5-A7CG 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7UC         TCGA-DG-A2KL 
"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-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-IR-A3LK         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                                             2
                    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
D20V32, 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)                                                                 2
  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"
D20V33, 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
D20V34, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                119 
        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-A3Y4 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A43B 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5FO         TCGA-EA-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EK-A2RA         TCGA-EK-A2RO 
"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-EX-A69M 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         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-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"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" 
D20V35, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                138 
        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-A2GZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2IP         TCGA-EK-A2PK         TCGA-EK-A2R7 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2R8         TCGA-EK-A2R9         TCGA-EK-A2RA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RC         TCGA-EK-A2RD         TCGA-EK-A2RE 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RJ         TCGA-EK-A2RK         TCGA-EK-A2RL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2RM         TCGA-EK-A2RN         TCGA-EK-A2RO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A3GJ         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-EX-A69M         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-A3TX         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" 
D20V36, 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
D20V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  C12ORF43 MUTATED              0           1          1
  C12ORF43 WILD-TYPE            8          42         45
D20V38, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 95 
        TCGA-C5-A1BI         TCGA-C5-A1BL         TCGA-C5-A1BN 
"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-A1MN         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-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HL 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7UH         TCGA-C5-A7X3 
"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-A7WF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A1QS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3HU         TCGA-EA-A3QD 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A3QE         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-A5O9 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EA-A5ZE         TCGA-EA-A5ZF         TCGA-EK-A2R7 
"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-EX-A69M 
"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" 
D20V39, continuous
D20V40, 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           2        14     1
D20V41, multiclass
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                 17 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1BN 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1MH         TCGA-C5-A1MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1MN         TCGA-C5-A1MQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LX         TCGA-C5-A2LY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-DS-A1OA         TCGA-DS-A3LQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-EK-A2H1         TCGA-HM-A3JJ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
D20V42, continuous
                    vv
clus                 T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  C12ORF43 MUTATED      0   0    1    0  0   0    0    0   1  1   0  0  0
  C12ORF43 WILD-TYPE    1  21   59   22  4   7    6   10  12  0   2  2  9
D20V43, multiclass
      clus
vv     C12ORF43 MUTATED C12ORF43 WILD-TYPE
  T1A1                0                  1
  T1B                 0                 21
  T1B1                1                 59
  T1B2                0                 22
  T2                  0                  4
  T2A                 0                  7
  T2A1                0                  6
  T2A2                0                 10
  T2B                 1                 12
  T3                  1                  0
  T3B                 0                  2
  T4                  0                  2
  TX                  0                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V44, 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
D20V45, 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(21) Variable = MED1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  MED1 MUTATED    11   0
  MED1 WILD-TYPE 139  40
  MED1 MUTATED MED1 WILD-TYPE 
            11            179 
  MED1 MUTATED MED1 WILD-TYPE 
             0             40 
$`MED1 MUTATED`
TCGA-C5-A1BJ TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A3HT TCGA-EA-A3Y4 
      144.16        58.88         2.66       117.99        31.36        14.50 
TCGA-EK-A2RE TCGA-IR-A3LH TCGA-LP-A5U2 TCGA-Q1-A5R3 TCGA-Q1-A73O 
        0.36        78.71         0.30        15.95        14.07 

$`MED1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       40.04        87.75        36.76       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        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
       37.35        30.90        33.30        13.05        25.02        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        14.50        26.01        12.66        12.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ 
        0.13        16.08         0.07         4.04         0.03         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         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-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        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       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.89        12.49         0.82        13.35        13.87        34.62 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       54.81        35.05        20.84        15.58        16.41         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        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  MED1 MUTATED MED1 WILD-TYPE 
          0.30           0.03 
  MED1 MUTATED MED1 WILD-TYPE 
        144.16         210.67 
  MED1 MUTATED MED1 WILD-TYPE 
         15.95          19.79 
[1] "0.3 - 144.2 (15.9)" "0.0 - 210.7 (19.8)"
[1] "hr="     "7.5e+07"
D21V2, continuous
                vv
clus              T1  T2 T3+T4
  MED1 MUTATED     4   4     0
  MED1 WILD-TYPE 100  36     5
D21V3, multiclass
       clus
vv      MED1 MUTATED MED1 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"
D21V4, binary
                cls
clus              0  1
  MED1 MUTATED    6  2
  MED1 WILD-TYPE 89 42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      6    2
  MED1 WILD-TYPE   89   42
   clus
vv  MED1 MUTATED MED1 WILD-TYPE
  0            6             89
  1            2             42
[1] 2 2
[1] FALSE
D21V5, binary
                cls
clus              0  1
  MED1 MUTATED    6  0
  MED1 WILD-TYPE 73  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      6    0
  MED1 WILD-TYPE   73    4
   clus
vv  MED1 MUTATED MED1 WILD-TYPE
  0            6             73
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  MED1 MUTATED               0                               10
  MED1 WILD-TYPE             4                              148
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  MED1 MUTATED                                               1
  MED1 WILD-TYPE                                             4
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  MED1 MUTATED                                     0
  MED1 WILD-TYPE                                  22
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  MED1 MUTATED                                           0
  MED1 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  MED1 MUTATED                                              0
  MED1 WILD-TYPE                                            3
D21V6, multiclass
                                               clus
vv                                              MED1 MUTATED MED1 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                        10            148
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            1              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D21V7, binary
                cls
clus               0   1
  MED1 MUTATED     2   9
  MED1 WILD-TYPE  30 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      2    9
  MED1 WILD-TYPE   30  153
     clus
vv    MED1 MUTATED MED1 WILD-TYPE
  NO             2             30
  YES            9            153
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED1 MUTATED                                  0     1
  MED1 WILD-TYPE                                8    18
                vv
clus             BLACK OR AFRICAN AMERICAN
  MED1 MUTATED                           1
  MED1 WILD-TYPE                        15
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MED1 MUTATED                                           0     8
  MED1 WILD-TYPE                                         1   130
D21V10, multiclass
                                           clus
vv                                          MED1 MUTATED MED1 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                                                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"
D21V11, binary
                cls
clus               0   1
  MED1 MUTATED     1   7
  MED1 WILD-TYPE  13 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      1    7
  MED1 WILD-TYPE   13  127
                        clus
vv                       MED1 MUTATED MED1 WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            7            127
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                cls
clus              0  1
  MED1 MUTATED    8  0
  MED1 WILD-TYPE 89 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      8    0
  MED1 WILD-TYPE   89   31
            clus
vv           MED1 MUTATED MED1 WILD-TYPE
  TUMOR FREE            8             89
  WITH TUMOR            0             31
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  MED1 MUTATED        0      1       1             8       1
  MED1 WILD-TYPE      5      9       5           151      13
D21V14, multiclass
               clus
vv              MED1 MUTATED MED1 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   1              9
  UKRAINE                  1              5
  UNITED STATES            8            151
  VIETNAM                  1             13
[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             G1 G2 G3 G4 GX
  MED1 MUTATED    1  5  3  1  1
  MED1 WILD-TYPE 13 83 79  0  7
D21V15, multiclass
    clus
vv   MED1 MUTATED MED1 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"
D21V16, continuous
[1] "Remove cluster labels:" "MED1 MUTATED"          
clus
  MED1 MUTATED MED1 WILD-TYPE 
             2             27 
    TCGA-BI-A0VR     TCGA-C5-A1BL     TCGA-C5-A1BQ     TCGA-C5-A1ME 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DS-A3LQ 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3TX 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
D21V17, continuous
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  MED1 MUTATED                                             2
  MED1 WILD-TYPE                                          24
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  MED1 MUTATED                                        0
  MED1 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  MED1 MUTATED                                                 0              1
  MED1 WILD-TYPE                                               1             36
                vv
clus             LIFELONG NON-SMOKER
  MED1 MUTATED                     7
  MED1 WILD-TYPE                  86
D21V18, multiclass
                                                 clus
vv                                                MED1 MUTATED MED1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                2             24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             1             36
  LIFELONG NON-SMOKER                                        7             86
[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"
D21V19, continuous
D21V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  MED1 MUTATED             1        4             1        0        0
  MED1 WILD-TYPE          19       50            11        1        7
D21V21, multiclass
               clus
vv              MED1 MUTATED MED1 WILD-TYPE
  COMBINATION              1             19
  EXTERNAL                 4             50
  EXTERNAL BEAM            1             11
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D21V22, binary
                cls
clus              0  1
  MED1 MUTATED    2  0
  MED1 WILD-TYPE 24  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      2    0
  MED1 WILD-TYPE   24    3
                         clus
vv                        MED1 MUTATED MED1 WILD-TYPE
  COMPLETED AS PLANNED               2             24
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  MED1 MUTATED                    0                0                   1
  MED1 WILD-TYPE                  2                2                  19
                vv
clus             REGIONAL SITE
  MED1 MUTATED               0
  MED1 WILD-TYPE             4
D21V23, multiclass
[1] "Remove cluster labels:" "MED1 MUTATED"          
clus
  MED1 MUTATED MED1 WILD-TYPE 
             1             27 
    TCGA-C5-A0TN     TCGA-C5-A1BF     TCGA-C5-A1BQ     TCGA-C5-A2LZ 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A7UE     TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-DS-A7WF     TCGA-EA-A43B     TCGA-EA-A5FO     TCGA-EX-A3L1 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-FU-A23L     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-IR-A3LF     TCGA-JW-A5VG     TCGA-JX-A3Q0 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-R2-A69V     TCGA-WL-A834 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
D21V24, binary
                cls
clus              0  1
  MED1 MUTATED    1  0
  MED1 WILD-TYPE 15  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      1    0
  MED1 WILD-TYPE   15    4
     clus
vv    MED1 MUTATED MED1 WILD-TYPE
  CGY            1             15
  GY             0              4
[1] 2 2
[1] FALSE
D21V25, continuous
D21V26, continuous
D21V27, continuous
D21V28, continuous
D21V29, continuous
D21V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MED1 MUTATED                                     0
  MED1 WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MED1 MUTATED                                     0                       3
  MED1 WILD-TYPE                                   7                      25
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MED1 MUTATED                         0                       1
  MED1 WILD-TYPE                       1                       5
D21V31, multiclass
                                     clus
vv                                    MED1 MUTATED MED1 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            0              7
  OTHER LOCATION, SPECIFY                        3             25
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              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)
  MED1 MUTATED                                               0
  MED1 WILD-TYPE                                             2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  MED1 MUTATED                                                0
  MED1 WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  MED1 MUTATED                                                                                   4
  MED1 WILD-TYPE                                                                                56
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  MED1 MUTATED                                                                                              7
  MED1 WILD-TYPE                                                                                           81
D21V32, multiclass
                                                                                              clus
vv                                                                                             MED1 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                                                                                             MED1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             2
  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"
D21V33, binary
                cls
clus              0  1
  MED1 MUTATED    4  5
  MED1 WILD-TYPE 59 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      4    5
  MED1 WILD-TYPE   59   62
         clus
vv        MED1 MUTATED MED1 WILD-TYPE
  ABSENT             4             59
  PRESENT            5             62
[1] 2 2
[1] FALSE
D21V34, continuous
D21V35, continuous
D21V36, binary
                cls
clus              0  1
  MED1 MUTATED    2  6
  MED1 WILD-TYPE 37 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      2    6
  MED1 WILD-TYPE   37   80
                                          clus
vv                                         MED1 MUTATED MED1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                2             37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            6             80
[1] 2 2
[1] FALSE
D21V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  MED1 MUTATED              0           4          3
  MED1 WILD-TYPE            8          39         43
D21V38, multiclass
              clus
vv             MED1 MUTATED MED1 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"
D21V39, continuous
D21V40, binary
                cls
clus              0  1
  MED1 MUTATED    8  1
  MED1 WILD-TYPE 80 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED1 MUTATED      8    1
  MED1 WILD-TYPE   80   15
         clus
vv        MED1 MUTATED MED1 WILD-TYPE
  ABSENT             8             80
  PRESENT            1             15
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  MED1 MUTATED             0         1     0
  MED1 WILD-TYPE           2        15     1
D21V41, multiclass
[1] "Remove cluster labels:" "MED1 MUTATED"          
clus
  MED1 MUTATED MED1 WILD-TYPE 
             1             18 
    TCGA-C5-A1BE     TCGA-C5-A1BI     TCGA-C5-A1BN     TCGA-C5-A1M9 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MK     TCGA-C5-A1MN 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LT     TCGA-C5-A2LX     TCGA-C5-A2LY 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EK-A2H0 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" "MED1 WILD-TYPE" 
    TCGA-EK-A2H1     TCGA-HM-A3JJ 
"MED1 WILD-TYPE" "MED1 WILD-TYPE" 
D21V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  MED1 MUTATED      0   2    2    0  0   1    1    1   1  0   0  0  2
  MED1 WILD-TYPE    1  19   58   22  4   6    5    9  12  1   2  2  7
D21V43, multiclass
      clus
vv     MED1 MUTATED MED1 WILD-TYPE
  T1A1            0              1
  T1B             2             19
  T1B1            2             58
  T1B2            0             22
  T2              0              4
  T2A             1              6
  T2A1            1              5
  T2A2            1              9
  T2B             1             12
  T3              0              1
  T3B             0              2
  T4              0              2
  TX              2              7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  MED1 MUTATED         0        0         0         0        4         0
  MED1 WILD-TYPE       4        1         1         1       24        53
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  MED1 MUTATED           1        0         1          1          0         1
  MED1 WILD-TYPE        28        4         5          4          7        13
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  MED1 MUTATED           0          2         0         0
  MED1 WILD-TYPE         1         27         2         5
D21V45, multiclass
            clus
vv           MED1 MUTATED MED1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              4             24
  STAGE IB1             0             53
  STAGE IB2             1             28
  STAGE II              0              4
  STAGE IIA             1              5
  STAGE IIA1            1              4
  STAGE IIA2            0              7
  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"

Clustering(22) Variable = USP28 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED     2   2
  USP28 WILD-TYPE 148  38
  USP28 MUTATED USP28 WILD-TYPE 
              4             186 
  USP28 MUTATED USP28 WILD-TYPE 
              2              38 
$`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-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
       40.04        87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       21.44        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 
      195.85        30.31         7.99        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        13.87        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        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  USP28 MUTATED USP28 WILD-TYPE 
          19.86            0.03 
  USP28 MUTATED USP28 WILD-TYPE 
         137.16          210.67 
  USP28 MUTATED USP28 WILD-TYPE 
         73.920          19.315 
[1] "19.9 - 137.2 (73.9)" "0.0 - 210.7 (19.3)" 
[1] "hr=" "1.1"
D22V2, continuous
                 vv
clus               T1  T2 T3+T4
  USP28 MUTATED     3   0     0
  USP28 WILD-TYPE 101  40     5
D22V3, 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"
D22V4, 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
D22V5, 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
                 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                                  22
                 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                                            3
D22V6, 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              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 1               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D22V7, binary
                 cls
clus                0   1
  USP28 MUTATED     0   4
  USP28 WILD-TYPE  32 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    4
  USP28 WILD-TYPE   32  158
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO              0              32
  YES             4             158
[1] 2 2
[1] FALSE
D22V8, 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" 
D22V9, 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
D22V10, 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"
D22V11, binary
                 cls
clus                0   1
  USP28 MUTATED     0   2
  USP28 WILD-TYPE  14 132
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    2
  USP28 WILD-TYPE   14  132
                        clus
vv                       USP28 MUTATED USP28 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             2             132
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                 cls
clus               0  1
  USP28 MUTATED    3  1
  USP28 WILD-TYPE 94 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3    1
  USP28 WILD-TYPE   94   30
            clus
vv           USP28 MUTATED USP28 WILD-TYPE
  TUMOR FREE             3              94
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  USP28 MUTATED        0      0       0             4       0
  USP28 WILD-TYPE      5     10       6           155      14
D22V14, multiclass
               clus
vv              USP28 MUTATED USP28 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             4             155
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  USP28 MUTATED    0  1  3  0  0
  USP28 WILD-TYPE 14 87 79  1  8
D22V15, 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"
D22V16, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              28 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1ME 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2      TCGA-C5-A3HD 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-DS-A3LQ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX 
"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" 
D22V17, 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" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  USP28 MUTATED                                             1
  USP28 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  USP28 MUTATED                                        0
  USP28 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  USP28 MUTATED                                                 0
  USP28 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  USP28 MUTATED                0                   3
  USP28 WILD-TYPE             37                  90
D22V18, multiclass
                                                 clus
vv                                                USP28 MUTATED USP28 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              0              37
  LIFELONG NON-SMOKER                                         3              90
[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"
D22V19, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              51 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME      TCGA-C5-A1MF 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MI      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-A7CL      TCGA-C5-A7CO 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DR-A0ZM      TCGA-DS-A5RQ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5      TCGA-FU-A2QG 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ      TCGA-FU-A3TX 
"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" 
D22V20, continuous
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              2              80 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1M6      TCGA-C5-A1M8 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A3HD      TCGA-C5-A3HF 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7UE      TCGA-C5-A7UH 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DG-A2KM      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VN 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WH 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A43B 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A5FO      TCGA-EA-A5O9 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EK-A2H0      TCGA-EX-A3L1      TCGA-EX-A449      TCGA-FU-A23L 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A3JK 
"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-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AU      TCGA-LP-A4AX      TCGA-LP-A7HU 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R2 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73O      TCGA-Q1-A73Q 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  USP28 MUTATED             0        3             0        0        0
  USP28 WILD-TYPE          20       51            12        1        7
D22V21, multiclass
               clus
vv              USP28 MUTATED USP28 WILD-TYPE
  COMBINATION               0              20
  EXTERNAL                  3              51
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D22V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  USP28 MUTATED                    0                0                   1
  USP28 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  USP28 MUTATED               0
  USP28 WILD-TYPE             4
D22V23, multiclass
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A2LZ      TCGA-C5-A7CK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DS-A7WF 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1      TCGA-FU-A23L 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
D22V24, binary
                 cls
clus               0  1
  USP28 MUTATED    0  0
  USP28 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    0
  USP28 WILD-TYPE   16    4
D22V25, continuous
D22V26, continuous
D22V27, continuous
D22V28, continuous
D22V29, continuous
D22V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  USP28 MUTATED                                     0
  USP28 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  USP28 MUTATED                                     1                       1
  USP28 WILD-TYPE                                   6                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  USP28 MUTATED                         0                       0
  USP28 WILD-TYPE                       1                       6
D22V31, multiclass
[1] "Remove cluster labels:" "USP28 MUTATED"         
clus
  USP28 MUTATED USP28 WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      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-A2M1      TCGA-C5-A3HE 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" "USP28 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"USP28 WILD-TYPE" "USP28 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  USP28 MUTATED                                               0
  USP28 WILD-TYPE                                             2
                 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
D22V32, 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)                                                              2
  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"
D22V33, 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
D22V34, continuous
D22V35, continuous
D22V36, 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
D22V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  USP28 MUTATED              0           1          2
  USP28 WILD-TYPE            8          42         44
D22V38, 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"
D22V39, continuous
D22V40, 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         0     0
  USP28 WILD-TYPE           2        16     1
D22V41, multiclass
D22V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  USP28 MUTATED      0   0    2    1  0   0    0    0   0  0   0  0  0
  USP28 WILD-TYPE    1  21   58   21  4   7    6   10  13  1   2  2  9
D22V43, multiclass
      clus
vv     USP28 MUTATED USP28 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             2              58
  T1B2             1              21
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              0              13
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V44, 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
D22V45, 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(23) Variable = IDS MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  IDS MUTATED     5   1
  IDS WILD-TYPE 145  39
  IDS MUTATED IDS WILD-TYPE 
            6           184 
  IDS MUTATED IDS WILD-TYPE 
            1            39 
$`IDS MUTATED`
TCGA-DS-A5RQ TCGA-EA-A3HU TCGA-EK-A2RB TCGA-EK-A2RC TCGA-FU-A3HZ TCGA-IR-A3LK 
       16.83        33.30         0.07         4.04        36.26        29.85 

$`IDS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-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        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        28.90        22.98        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        12.36        37.35        30.90        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17        31.36         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         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       117.40        96.95        78.71        81.96 
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       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        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        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
        3.88        11.67        93.99        26.01 

  IDS MUTATED IDS WILD-TYPE 
         0.07          0.03 
  IDS MUTATED IDS WILD-TYPE 
        36.26        210.67 
  IDS MUTATED IDS WILD-TYPE 
        23.34         19.69 
[1] "0.1 - 36.3 (23.3)"  "0.0 - 210.7 (19.7)"
[1] "hr=" "1.2"
D23V2, continuous
               vv
clus             T1  T2 T3+T4
  IDS MUTATED     2   2     0
  IDS WILD-TYPE 102  38     5
D23V3, multiclass
       clus
vv      IDS MUTATED IDS WILD-TYPE
  T1              2           102
  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"
D23V4, binary
               cls
clus             0  1
  IDS MUTATED    4  0
  IDS WILD-TYPE 91 44
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      4    0
  IDS WILD-TYPE   91   44
   clus
vv  IDS MUTATED IDS WILD-TYPE
  0           4            91
  1           0            44
[1] 2 2
[1] FALSE
D23V5, binary
               cls
clus             0  1
  IDS MUTATED    3  0
  IDS WILD-TYPE 76  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      3    0
  IDS WILD-TYPE   76    4
   clus
vv  IDS MUTATED IDS WILD-TYPE
  0           3            76
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  IDS MUTATED               0                                6
  IDS WILD-TYPE             4                              152
               vv
clus            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  IDS MUTATED                                               0
  IDS WILD-TYPE                                             5
               vv
clus            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  IDS MUTATED                                     1
  IDS WILD-TYPE                                  21
               vv
clus            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  IDS MUTATED                                           0
  IDS WILD-TYPE                                         2
               vv
clus            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  IDS MUTATED                                              0
  IDS WILD-TYPE                                            3
D23V6, multiclass
                                               clus
vv                                              IDS MUTATED IDS WILD-TYPE
  ADENOSQUAMOUS                                           0             4
  CERVICAL SQUAMOUS CELL CARCINOMA                        6           152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE           0             5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                     1            21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX               0             2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE            0             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"
D23V7, binary
               cls
clus              0   1
  IDS MUTATED     0   7
  IDS WILD-TYPE  32 155
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      0    7
  IDS WILD-TYPE   32  155
     clus
vv    IDS MUTATED IDS WILD-TYPE
  NO            0            32
  YES           7           155
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            1            56 
   TCGA-BI-A0VR    TCGA-C5-A1BF    TCGA-C5-A1BI    TCGA-C5-A1BJ    TCGA-C5-A1BL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1BN    TCGA-C5-A1BQ    TCGA-C5-A1M7    TCGA-C5-A1ME    TCGA-C5-A1MF 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1MH    TCGA-C5-A1MI    TCGA-C5-A1ML    TCGA-C5-A1MN    TCGA-C5-A2LS 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2LZ    TCGA-C5-A2M2 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A3HD    TCGA-C5-A3HF    TCGA-C5-A7CJ    TCGA-C5-A7CK    TCGA-C5-A7CL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7CO    TCGA-C5-A7UE    TCGA-DG-A2KK    TCGA-DG-A2KL    TCGA-DR-A0ZM 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DS-A7WF    TCGA-EA-A556    TCGA-EX-A1H5    TCGA-FU-A2QG    TCGA-FU-A3EO 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A3HY    TCGA-FU-A3TQ    TCGA-FU-A3WB    TCGA-FU-A3YQ    TCGA-FU-A5XV 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A770    TCGA-HM-A4S6    TCGA-HM-A6W2    TCGA-IR-A3L7    TCGA-IR-A3LB 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LH    TCGA-JW-A5VI    TCGA-JW-A5VK    TCGA-JX-A3Q0    TCGA-MU-A5YI 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-Q1-A6DW    TCGA-Q1-A73Q    TCGA-Q1-A73S    TCGA-RA-A741    TCGA-UC-A7PD 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-WL-A834 
"IDS WILD-TYPE" 
D23V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDS MUTATED                                  0     0
  IDS WILD-TYPE                                8    19
               vv
clus            BLACK OR AFRICAN AMERICAN
  IDS MUTATED                           0
  IDS WILD-TYPE                        16
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IDS MUTATED                                           0     6
  IDS WILD-TYPE                                         1   132
D23V10, multiclass
                                           clus
vv                                          IDS MUTATED IDS 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                                               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"
D23V11, binary
               cls
clus              0   1
  IDS MUTATED     1   4
  IDS WILD-TYPE  13 130
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      1    4
  IDS WILD-TYPE   13  130
                        clus
vv                       IDS MUTATED IDS WILD-TYPE
  HISPANIC OR LATINO               1            13
  NOT HISPANIC OR LATINO           4           130
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
               cls
clus             0  1
  IDS MUTATED    3  1
  IDS WILD-TYPE 94 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      3    1
  IDS WILD-TYPE   94   30
            clus
vv           IDS MUTATED IDS WILD-TYPE
  TUMOR FREE           3            94
  WITH TUMOR           1            30
[1] 2 2
[1] FALSE
               vv
clus            CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  IDS MUTATED        0      1       0             6       0
  IDS WILD-TYPE      5      9       6           153      14
D23V14, multiclass
               clus
vv              IDS MUTATED IDS WILD-TYPE
  CANADA                  0             5
  RUSSIA                  1             9
  UKRAINE                 0             6
  UNITED STATES           6           153
  VIETNAM                 0            14
[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            G1 G2 G3 G4 GX
  IDS MUTATED    0  3  4  0  0
  IDS WILD-TYPE 14 85 78  1  8
D23V15, multiclass
    clus
vv   IDS MUTATED IDS WILD-TYPE
  G1           0            14
  G2           3            85
  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"
D23V16, continuous
D23V17, continuous
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            1            56 
   TCGA-BI-A0VR    TCGA-C5-A1BF    TCGA-C5-A1BI    TCGA-C5-A1BJ    TCGA-C5-A1BL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1BN    TCGA-C5-A1BQ    TCGA-C5-A1M7    TCGA-C5-A1ME    TCGA-C5-A1MF 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1MH    TCGA-C5-A1MI    TCGA-C5-A1ML    TCGA-C5-A1MN    TCGA-C5-A2LS 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2LZ    TCGA-C5-A2M2 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A3HD    TCGA-C5-A3HF    TCGA-C5-A7CJ    TCGA-C5-A7CK    TCGA-C5-A7CL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7CO    TCGA-C5-A7UE    TCGA-DG-A2KK    TCGA-DG-A2KL    TCGA-DR-A0ZM 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DS-A7WF    TCGA-EA-A556    TCGA-EX-A1H5    TCGA-FU-A2QG    TCGA-FU-A3EO 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A3HY    TCGA-FU-A3TQ    TCGA-FU-A3WB    TCGA-FU-A3YQ    TCGA-FU-A5XV 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A770    TCGA-HM-A4S6    TCGA-HM-A6W2    TCGA-IR-A3L7    TCGA-IR-A3LB 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LH    TCGA-JW-A5VI    TCGA-JW-A5VK    TCGA-JX-A3Q0    TCGA-MU-A5YI 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-Q1-A6DW    TCGA-Q1-A73Q    TCGA-Q1-A73S    TCGA-RA-A741    TCGA-UC-A7PD 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-WL-A834 
"IDS WILD-TYPE" 
               vv
clus            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  IDS MUTATED                                             0
  IDS WILD-TYPE                                          26
               vv
clus            CURRENT REFORMED SMOKER FOR > 15 YEARS
  IDS MUTATED                                        0
  IDS WILD-TYPE                                      8
               vv
clus            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  IDS MUTATED                                                 0              2
  IDS WILD-TYPE                                               1             35
               vv
clus            LIFELONG NON-SMOKER
  IDS MUTATED                     4
  IDS WILD-TYPE                  89
D23V18, multiclass
                                                 clus
vv                                                IDS MUTATED IDS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS               0            26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                    0             8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED           0             1
  CURRENT SMOKER                                            2            35
  LIFELONG NON-SMOKER                                       4            89
[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"
D23V19, continuous
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            1            51 
   TCGA-BI-A0VR    TCGA-C5-A1BI    TCGA-C5-A1BJ    TCGA-C5-A1BL    TCGA-C5-A1BN 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1BQ    TCGA-C5-A1M7    TCGA-C5-A1ME    TCGA-C5-A1MF    TCGA-C5-A1MI 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2LS    TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2LZ 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2M2    TCGA-C5-A3HD    TCGA-C5-A3HF    TCGA-C5-A7CJ    TCGA-C5-A7CL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7CO    TCGA-C5-A7UE    TCGA-DG-A2KK    TCGA-DR-A0ZM    TCGA-EA-A556 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EK-A2RA    TCGA-EX-A1H5    TCGA-FU-A2QG    TCGA-FU-A3EO    TCGA-FU-A3HY 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A3TQ    TCGA-FU-A3TX    TCGA-FU-A3WB    TCGA-FU-A3YQ    TCGA-FU-A5XV 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A770    TCGA-HM-A4S6    TCGA-HM-A6W2    TCGA-IR-A3L7    TCGA-IR-A3LB 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LH    TCGA-JW-A5VI    TCGA-JW-A5VK    TCGA-JX-A3Q0    TCGA-MU-A5YI 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-Q1-A6DW    TCGA-Q1-A73Q    TCGA-Q1-A73S    TCGA-RA-A741    TCGA-UC-A7PD 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-WL-A834 
"IDS WILD-TYPE" 
D23V20, continuous
               vv
clus            COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  IDS MUTATED             0        3             0        0        0
  IDS WILD-TYPE          20       51            12        1        7
D23V21, multiclass
               clus
vv              IDS MUTATED IDS WILD-TYPE
  COMBINATION             0            20
  EXTERNAL                3            51
  EXTERNAL BEAM           0            12
  IMPLANTS                0             1
  INTERNAL                0             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"
D23V22, binary
               cls
clus             0  1
  IDS MUTATED    0  0
  IDS WILD-TYPE 26  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      0    0
  IDS WILD-TYPE   26    3
               vv
clus            DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  IDS MUTATED                    0                0                   1
  IDS WILD-TYPE                  2                2                  19
               vv
clus            REGIONAL SITE
  IDS MUTATED               0
  IDS WILD-TYPE             4
D23V23, multiclass
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            1            27 
   TCGA-C5-A0TN    TCGA-C5-A1BF    TCGA-C5-A1BQ    TCGA-C5-A2LZ    TCGA-C5-A7CK 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7CL    TCGA-C5-A7CM    TCGA-C5-A7CO    TCGA-C5-A7UE    TCGA-C5-A7UH 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7X3    TCGA-DG-A2KL    TCGA-DS-A7WF    TCGA-EA-A43B    TCGA-EA-A5FO 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EX-A3L1    TCGA-FU-A23L    TCGA-FU-A3HY    TCGA-HM-A3JJ    TCGA-HM-A4S6 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LF    TCGA-IR-A3LH    TCGA-JW-A5VG    TCGA-JX-A3Q0    TCGA-JX-A5QV 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-R2-A69V    TCGA-WL-A834 
"IDS WILD-TYPE" "IDS WILD-TYPE" 
D23V24, binary
               cls
clus             0  1
  IDS MUTATED    1  0
  IDS WILD-TYPE 15  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      1    0
  IDS WILD-TYPE   15    4
     clus
vv    IDS MUTATED IDS WILD-TYPE
  CGY           1            15
  GY            0             4
[1] 2 2
[1] FALSE
D23V25, continuous
D23V26, continuous
D23V27, continuous
D23V28, continuous
D23V29, continuous
D23V30, continuous
               vv
clus            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  IDS MUTATED                                     0
  IDS WILD-TYPE                                   2
               vv
clus            MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  IDS MUTATED                                     1                       0
  IDS WILD-TYPE                                   6                      28
               vv
clus            POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  IDS MUTATED                         0                       0
  IDS WILD-TYPE                       1                       6
D23V31, multiclass
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            1            43 
   TCGA-BI-A20A    TCGA-C5-A0TN    TCGA-C5-A1BE    TCGA-C5-A1BK    TCGA-C5-A1BM 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1M5    TCGA-C5-A1M7    TCGA-C5-A1M8    TCGA-C5-A1M9    TCGA-C5-A1ME 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1MF    TCGA-C5-A1MJ    TCGA-C5-A1MP    TCGA-C5-A1MQ    TCGA-C5-A2LS 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2M1    TCGA-C5-A3HE 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A3HL    TCGA-C5-A7CG    TCGA-C5-A7CJ    TCGA-C5-A7UC    TCGA-DG-A2KL 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DR-A0ZM    TCGA-DS-A0VK    TCGA-DS-A0VL    TCGA-DS-A0VM    TCGA-DS-A0VN 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DS-A1OA    TCGA-DS-A3LQ    TCGA-EA-A50E    TCGA-EK-A2RN    TCGA-EK-A2RO 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EX-A1H5    TCGA-EX-A449    TCGA-FU-A3EO    TCGA-HM-A4S6    TCGA-IR-A3LH 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LI    TCGA-UC-A7PD    TCGA-WL-A834 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
               vv
clus            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  IDS MUTATED                                               0
  IDS WILD-TYPE                                             2
               vv
clus            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  IDS MUTATED                                                0
  IDS WILD-TYPE                                             10
               vv
clus            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  IDS MUTATED                                                                                   4
  IDS WILD-TYPE                                                                                56
               vv
clus            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  IDS MUTATED                                                                                              1
  IDS WILD-TYPE                                                                                           87
D23V32, multiclass
                                                                                              clus
vv                                                                                             IDS 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)           1
                                                                                              clus
vv                                                                                             IDS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                            2
  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)            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"
D23V33, binary
               cls
clus             0  1
  IDS MUTATED    2  3
  IDS WILD-TYPE 61 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      2    3
  IDS WILD-TYPE   61   64
         clus
vv        IDS MUTATED IDS WILD-TYPE
  ABSENT            2            61
  PRESENT           3            64
[1] 2 2
[1] FALSE
D23V34, continuous
D23V35, continuous
D23V36, binary
               cls
clus             0  1
  IDS MUTATED    1  2
  IDS WILD-TYPE 38 84
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      1    2
  IDS WILD-TYPE   38   84
                                          clus
vv                                         IDS MUTATED IDS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA               1            38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA           2            84
[1] 2 2
[1] FALSE
D23V37, continuous
               vv
clus            CURRENT USER FORMER USER NEVER USED
  IDS MUTATED              0           0          2
  IDS WILD-TYPE            8          43         44
D23V38, multiclass
[1] "Remove cluster labels:" "IDS MUTATED"           
clus
  IDS MUTATED IDS WILD-TYPE 
            2            95 
   TCGA-C5-A1BI    TCGA-C5-A1BL    TCGA-C5-A1BN    TCGA-C5-A1M6    TCGA-C5-A1M7 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A1M8    TCGA-C5-A1M9    TCGA-C5-A1ME    TCGA-C5-A1MF    TCGA-C5-A1MN 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2LT    TCGA-C5-A2LV    TCGA-C5-A2LX    TCGA-C5-A2LY    TCGA-C5-A2M1 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A2M2    TCGA-C5-A3HD    TCGA-C5-A3HL    TCGA-C5-A7CG    TCGA-C5-A7UH 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-C5-A7X3    TCGA-DG-A2KM    TCGA-DR-A0ZL    TCGA-DR-A0ZM    TCGA-DS-A0VK 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DS-A0VL    TCGA-DS-A0VM    TCGA-DS-A0VN    TCGA-DS-A1OA    TCGA-DS-A3LQ 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-DS-A7WF    TCGA-DS-A7WH    TCGA-DS-A7WI    TCGA-EA-A1QS    TCGA-EA-A1QT 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EA-A3HQ    TCGA-EA-A3HR    TCGA-EA-A3HT    TCGA-EA-A3QD    TCGA-EA-A3QE 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EA-A410    TCGA-EA-A411    TCGA-EA-A43B    TCGA-EA-A44S    TCGA-EA-A4BA 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EA-A50E    TCGA-EA-A556    TCGA-EA-A5O9    TCGA-EA-A5ZE    TCGA-EA-A5ZF 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EK-A2R7    TCGA-EK-A3GK    TCGA-EX-A1H5    TCGA-EX-A1H6    TCGA-EX-A3L1 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-EX-A69L    TCGA-EX-A69M    TCGA-FU-A2QG    TCGA-FU-A3EO    TCGA-FU-A3HY 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-FU-A3WB    TCGA-FU-A3YQ    TCGA-FU-A57G    TCGA-FU-A770    TCGA-HM-A3JJ 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-HM-A3JK    TCGA-HM-A4S6    TCGA-HM-A6W2    TCGA-IR-A3L7    TCGA-IR-A3LA 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-IR-A3LB    TCGA-IR-A3LC    TCGA-IR-A3LF    TCGA-IR-A3LH    TCGA-IR-A3LI 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-JW-A5VG    TCGA-JW-A5VI    TCGA-JW-A5VJ    TCGA-JW-A5VK    TCGA-JW-A69B 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-JX-A3PZ    TCGA-JX-A3Q0    TCGA-JX-A3Q8    TCGA-JX-A5QV    TCGA-LP-A5U2 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-LP-A5U3    TCGA-LP-A7HU    TCGA-Q1-A5R1    TCGA-Q1-A5R2    TCGA-Q1-A5R3 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
   TCGA-Q1-A6DV    TCGA-Q1-A73P    TCGA-Q1-A73S    TCGA-UC-A7PD    TCGA-WL-A834 
"IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" "IDS WILD-TYPE" 
D23V39, continuous
D23V40, binary
               cls
clus             0  1
  IDS MUTATED    4  1
  IDS WILD-TYPE 84 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDS MUTATED      4    1
  IDS WILD-TYPE   84   15
         clus
vv        IDS MUTATED IDS WILD-TYPE
  ABSENT            4            84
  PRESENT           1            15
[1] 2 2
[1] FALSE
               vv
clus            CARBOPLATIN CISPLATIN OTHER
  IDS MUTATED             0         0     0
  IDS WILD-TYPE           2        16     1
D23V41, multiclass
D23V42, continuous
               vv
clus            T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  IDS MUTATED      0   0    1    1  0   0    0    2   0  0   0  0  0
  IDS WILD-TYPE    1  21   59   21  4   7    6    8  13  1   2  2  9
D23V43, multiclass
      clus
vv     IDS MUTATED IDS WILD-TYPE
  T1A1           0             1
  T1B            0            21
  T1B1           1            59
  T1B2           1            21
  T2             0             4
  T2A            0             7
  T2A1           0             6
  T2A2           2             8
  T2B            0            13
  T3             0             1
  T3B            0             2
  T4             0             2
  TX             0             9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V44, continuous
               vv
clus            STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  IDS MUTATED         0        0         0         0        0         2
  IDS WILD-TYPE       4        1         1         1       28        51
               vv
clus            STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  IDS MUTATED           1        1         1          0          1         0
  IDS WILD-TYPE        28        3         5          5          6        14
               vv
clus            STAGE III STAGE IIIB STAGE IVA STAGE IVB
  IDS MUTATED           0          0         0         1
  IDS WILD-TYPE         1         29         2         4
D23V45, multiclass
            clus
vv           IDS MUTATED IDS 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            1            28
  STAGE II             1             3
  STAGE IIA            1             5
  STAGE IIA1           0             5
  STAGE IIA2           1             6
  STAGE IIB            0            14
  STAGE III            0             1
  STAGE IIIB           0            29
  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(24) Variable = TRIM9 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  TRIM9 MUTATED     6   2
  TRIM9 WILD-TYPE 144  38
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              8             182 
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              2              38 
$`TRIM9 MUTATED`
TCGA-C5-A1MJ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-DS-A0VN TCGA-IR-A3LA TCGA-JW-A5VL 
        0.46        33.24        52.01       118.65       137.16        15.58 
TCGA-JX-A3Q0 TCGA-Q1-A73O 
      195.85        14.07 

$`TRIM9 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF 
       83.05        78.35       100.14        38.43        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        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1OA TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99        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        12.36 
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 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51        19.27         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        47.77         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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-A3LH TCGA-IR-A3LI 
      147.39        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        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        30.31         7.99 
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 
       13.87        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-A73P 
       16.41        15.95         9.04        16.14        17.56        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        15.39        19.36        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-WL-A834 
       93.99        26.01 

  TRIM9 MUTATED TRIM9 WILD-TYPE 
           0.46            0.03 
  TRIM9 MUTATED TRIM9 WILD-TYPE 
         195.85          210.67 
  TRIM9 MUTATED TRIM9 WILD-TYPE 
         42.625          19.475 
[1] "0.5 - 195.8 (42.6)" "0.0 - 210.7 (19.5)"
[1] "hr=" "1.6"
D24V2, continuous
                 vv
clus               T1  T2 T3+T4
  TRIM9 MUTATED     4   0     1
  TRIM9 WILD-TYPE 100  40     4
D24V3, multiclass
       clus
vv      TRIM9 MUTATED TRIM9 WILD-TYPE
  T1                4             100
  T2                0              40
  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"
D24V4, binary
                 cls
clus               0  1
  TRIM9 MUTATED    4  0
  TRIM9 WILD-TYPE 91 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      4    0
  TRIM9 WILD-TYPE   91   44
   clus
vv  TRIM9 MUTATED TRIM9 WILD-TYPE
  0             4              91
  1             0              44
[1] 2 2
[1] FALSE
D24V5, binary
                 cls
clus               0  1
  TRIM9 MUTATED    3  0
  TRIM9 WILD-TYPE 76  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      3    0
  TRIM9 WILD-TYPE   76    4
   clus
vv  TRIM9 MUTATED TRIM9 WILD-TYPE
  0             3              76
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  TRIM9 MUTATED               0                                5
  TRIM9 WILD-TYPE             4                              153
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  TRIM9 MUTATED                                               0
  TRIM9 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  TRIM9 MUTATED                                     2
  TRIM9 WILD-TYPE                                  20
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  TRIM9 MUTATED                                           1
  TRIM9 WILD-TYPE                                         1
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  TRIM9 MUTATED                                              0
  TRIM9 WILD-TYPE                                            3
D24V6, multiclass
                                               clus
vv                                              TRIM9 MUTATED TRIM9 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          5             153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       2              20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 1               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D24V7, binary
                 cls
clus                0   1
  TRIM9 MUTATED     2   6
  TRIM9 WILD-TYPE  30 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      2    6
  TRIM9 WILD-TYPE   30  156
     clus
vv    TRIM9 MUTATED TRIM9 WILD-TYPE
  NO              2              30
  YES             6             156
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM9 MUTATED                                  1     0
  TRIM9 WILD-TYPE                                7    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  TRIM9 MUTATED                           1
  TRIM9 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIM9 MUTATED                                           0     5
  TRIM9 WILD-TYPE                                         1   133
D24V10, multiclass
                                           clus
vv                                          TRIM9 MUTATED TRIM9 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                                                 5             133
[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"
D24V11, binary
                 cls
clus                0   1
  TRIM9 MUTATED     2   4
  TRIM9 WILD-TYPE  12 130
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      2    4
  TRIM9 WILD-TYPE   12  130
                        clus
vv                       TRIM9 MUTATED TRIM9 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO             4             130
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                 cls
clus               0  1
  TRIM9 MUTATED    7  0
  TRIM9 WILD-TYPE 90 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      7    0
  TRIM9 WILD-TYPE   90   31
            clus
vv           TRIM9 MUTATED TRIM9 WILD-TYPE
  TUMOR FREE             7              90
  WITH TUMOR             0              31
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  TRIM9 MUTATED        0      0       0             8       0
  TRIM9 WILD-TYPE      5     10       6           151      14
D24V14, multiclass
               clus
vv              TRIM9 MUTATED TRIM9 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             8             151
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  TRIM9 MUTATED    1  5  1  0  1
  TRIM9 WILD-TYPE 13 83 81  1  7
D24V15, multiclass
    clus
vv   TRIM9 MUTATED TRIM9 WILD-TYPE
  G1             1              13
  G2             5              83
  G3             1              81
  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"
D24V16, continuous
D24V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  TRIM9 MUTATED                                             3
  TRIM9 WILD-TYPE                                          23
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  TRIM9 MUTATED                                        0
  TRIM9 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  TRIM9 MUTATED                                                 0
  TRIM9 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  TRIM9 MUTATED                0                   5
  TRIM9 WILD-TYPE             37                  88
D24V18, multiclass
                                                 clus
vv                                                TRIM9 MUTATED TRIM9 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 3              23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              0              37
  LIFELONG NON-SMOKER                                         5              88
[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"
D24V19, continuous
D24V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  TRIM9 MUTATED             1        3             1        0        0
  TRIM9 WILD-TYPE          19       51            11        1        7
D24V21, multiclass
               clus
vv              TRIM9 MUTATED TRIM9 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  3              51
  EXTERNAL BEAM             1              11
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D24V22, binary
                 cls
clus               0  1
  TRIM9 MUTATED    1  0
  TRIM9 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      1    0
  TRIM9 WILD-TYPE   25    3
                         clus
vv                        TRIM9 MUTATED TRIM9 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  TRIM9 MUTATED                    0                0                   1
  TRIM9 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  TRIM9 MUTATED               0
  TRIM9 WILD-TYPE             4
D24V23, multiclass
[1] "Remove cluster labels:" "TRIM9 MUTATED"         
clus
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
D24V24, binary
                 cls
clus               0  1
  TRIM9 MUTATED    1  0
  TRIM9 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      1    0
  TRIM9 WILD-TYPE   15    4
     clus
vv    TRIM9 MUTATED TRIM9 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D24V25, continuous
D24V26, continuous
D24V27, continuous
D24V28, continuous
D24V29, continuous
D24V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  TRIM9 MUTATED                                     0
  TRIM9 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  TRIM9 MUTATED                                     0                       2
  TRIM9 WILD-TYPE                                   7                      26
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  TRIM9 MUTATED                         0                       0
  TRIM9 WILD-TYPE                       1                       6
D24V31, multiclass
[1] "Remove cluster labels:" "TRIM9 MUTATED"         
clus
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MP 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE      TCGA-C5-A3HL 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-DG-A2KL 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E      TCGA-EK-A2RN 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449      TCGA-FU-A3EO 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  TRIM9 MUTATED                                               0
  TRIM9 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  TRIM9 MUTATED                                                0
  TRIM9 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  TRIM9 MUTATED                                                                                   4
  TRIM9 WILD-TYPE                                                                                56
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  TRIM9 MUTATED                                                                                              3
  TRIM9 WILD-TYPE                                                                                           85
D24V32, multiclass
                                                                                              clus
vv                                                                                             TRIM9 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                                                                                             TRIM9 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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"
D24V33, binary
                 cls
clus               0  1
  TRIM9 MUTATED    2  2
  TRIM9 WILD-TYPE 61 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      2    2
  TRIM9 WILD-TYPE   61   65
         clus
vv        TRIM9 MUTATED TRIM9 WILD-TYPE
  ABSENT              2              61
  PRESENT             2              65
[1] 2 2
[1] FALSE
D24V34, continuous
D24V35, continuous
D24V36, binary
                 cls
clus               0  1
  TRIM9 MUTATED    2  2
  TRIM9 WILD-TYPE 37 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      2    2
  TRIM9 WILD-TYPE   37   84
                                          clus
vv                                         TRIM9 MUTATED TRIM9 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 2              37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             2              84
[1] 2 2
[1] FALSE
D24V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  TRIM9 MUTATED              0           3          2
  TRIM9 WILD-TYPE            8          40         44
D24V38, multiclass
              clus
vv             TRIM9 MUTATED TRIM9 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"
D24V39, continuous
D24V40, binary
                 cls
clus               0  1
  TRIM9 MUTATED    4  0
  TRIM9 WILD-TYPE 84 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM9 MUTATED      4    0
  TRIM9 WILD-TYPE   84   16
         clus
vv        TRIM9 MUTATED TRIM9 WILD-TYPE
  ABSENT              4              84
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  TRIM9 MUTATED             0         1     0
  TRIM9 WILD-TYPE           2        15     1
D24V41, multiclass
[1] "Remove cluster labels:" "TRIM9 MUTATED"         
clus
  TRIM9 MUTATED TRIM9 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"TRIM9 WILD-TYPE" "TRIM9 WILD-TYPE" 
D24V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  TRIM9 MUTATED      0   0    2    2  0   0    0    0   0  1   0  0  1
  TRIM9 WILD-TYPE    1  21   58   20  4   7    6   10  13  0   2  2  8
D24V43, multiclass
      clus
vv     TRIM9 MUTATED TRIM9 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             2              58
  T1B2             2              20
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              0              13
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               1               8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  TRIM9 MUTATED         0        0         0         0        1         2
  TRIM9 WILD-TYPE       4        1         1         1       27        51
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  TRIM9 MUTATED           3        0         0          0          0         1
  TRIM9 WILD-TYPE        26        4         6          5          7        13
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  TRIM9 MUTATED           1          0         0         0
  TRIM9 WILD-TYPE         0         29         2         5
D24V45, multiclass
            clus
vv           TRIM9 MUTATED TRIM9 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              2              51
  STAGE IB2              3              26
  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             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(25) Variable = SEMA4B MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  SEMA4B MUTATED     3   4
  SEMA4B WILD-TYPE 147  36
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               7              183 
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               4               36 
$`SEMA4B MUTATED`
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A3HE TCGA-EK-A2PG TCGA-EK-A3GJ 
       68.84        18.74        19.86        18.02         1.51         0.10 
TCGA-IR-A3LK 
       29.85 

$`SEMA4B WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        23.67        11.44        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-DR-A0ZM 
       58.88        50.76        44.94        40.04        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       36.76         2.66       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        12.36 
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 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         7.46        14.89        26.79        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64        19.27         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        47.77         2.24         0.10         0.07 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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-A3LL 
       66.81       117.40        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-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       195.85        30.31         7.99 
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 
       13.87        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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  SEMA4B MUTATED SEMA4B WILD-TYPE 
            0.10             0.03 
  SEMA4B MUTATED SEMA4B WILD-TYPE 
           68.84           210.67 
  SEMA4B MUTATED SEMA4B WILD-TYPE 
           18.74            19.79 
[1] "0.1 - 68.8 (18.7)"  "0.0 - 210.7 (19.8)"
[1] "hr=" "4.1"
D25V2, continuous
                  vv
clus                T1  T2 T3+T4
  SEMA4B MUTATED     4   0     0
  SEMA4B WILD-TYPE 100  40     5
D25V3, multiclass
       clus
vv      SEMA4B MUTATED SEMA4B WILD-TYPE
  T1                 4              100
  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"
D25V4, binary
                  cls
clus                0  1
  SEMA4B MUTATED    4  1
  SEMA4B WILD-TYPE 91 43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      4    1
  SEMA4B WILD-TYPE   91   43
   clus
vv  SEMA4B MUTATED SEMA4B WILD-TYPE
  0              4               91
  1              1               43
[1] 2 2
[1] FALSE
D25V5, binary
                  cls
clus                0  1
  SEMA4B MUTATED    2  0
  SEMA4B WILD-TYPE 77  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      2    0
  SEMA4B WILD-TYPE   77    4
   clus
vv  SEMA4B MUTATED SEMA4B WILD-TYPE
  0              2               77
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  SEMA4B MUTATED               0                                7
  SEMA4B WILD-TYPE             4                              151
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  SEMA4B MUTATED                                               0
  SEMA4B WILD-TYPE                                             5
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  SEMA4B MUTATED                                     0
  SEMA4B WILD-TYPE                                  22
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  SEMA4B MUTATED                                           0
  SEMA4B WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  SEMA4B MUTATED                                              0
  SEMA4B WILD-TYPE                                            3
D25V6, multiclass
                                               clus
vv                                              SEMA4B MUTATED SEMA4B WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           7              151
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              0                5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        0               22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D25V7, binary
                  cls
clus                 0   1
  SEMA4B MUTATED     2   5
  SEMA4B WILD-TYPE  30 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      2    5
  SEMA4B WILD-TYPE   30  157
     clus
vv    SEMA4B MUTATED SEMA4B WILD-TYPE
  NO               2               30
  YES              5              157
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ       TCGA-C5-A1BL 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M7       TCGA-C5-A1ME       TCGA-C5-A1MF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML       TCGA-C5-A1MN 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD       TCGA-C5-A3HF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CO 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DR-A0ZM 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEMA4B MUTATED                                  0     0
  SEMA4B WILD-TYPE                                8    19
                  vv
clus               BLACK OR AFRICAN AMERICAN
  SEMA4B MUTATED                           1
  SEMA4B WILD-TYPE                        15
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SEMA4B MUTATED                                           1     5
  SEMA4B WILD-TYPE                                         0   133
D25V10, multiclass
                                           clus
vv                                          SEMA4B MUTATED SEMA4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                8
  ASIAN                                                  0               19
  BLACK OR AFRICAN AMERICAN                              1               15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                  5              133
[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"
D25V11, binary
                  cls
clus                 0   1
  SEMA4B MUTATED     0   2
  SEMA4B WILD-TYPE  14 132
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      0    2
  SEMA4B WILD-TYPE   14  132
                        clus
vv                       SEMA4B MUTATED SEMA4B WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              2              132
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                  cls
clus                0  1
  SEMA4B MUTATED    1  3
  SEMA4B WILD-TYPE 96 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      1    3
  SEMA4B WILD-TYPE   96   28
            clus
vv           SEMA4B MUTATED SEMA4B WILD-TYPE
  TUMOR FREE              1               96
  WITH TUMOR              3               28
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  SEMA4B MUTATED        0      0       0             7       0
  SEMA4B WILD-TYPE      5     10       6           152      14
D25V14, multiclass
               clus
vv              SEMA4B MUTATED SEMA4B WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    0                6
  UNITED STATES              7              152
  VIETNAM                    0               14
[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               G1 G2 G3 G4 GX
  SEMA4B MUTATED    1  2  4  0  0
  SEMA4B WILD-TYPE 13 86 78  1  8
D25V15, multiclass
    clus
vv   SEMA4B MUTATED SEMA4B WILD-TYPE
  G1              1               13
  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"
D25V16, continuous
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               1               28 
      TCGA-BI-A0VR       TCGA-C5-A1BJ       TCGA-C5-A1BL       TCGA-C5-A1ME 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A2M2       TCGA-C5-A3HD 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-DG-A2KK       TCGA-DS-A3LQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3TX 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-IR-A3L7 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-JX-A3Q0       TCGA-MU-A5YI 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V17, continuous
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ       TCGA-C5-A1BL 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M7       TCGA-C5-A1ME       TCGA-C5-A1MF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML       TCGA-C5-A1MN 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD       TCGA-C5-A3HF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CO 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DR-A0ZM 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  SEMA4B MUTATED                                             1
  SEMA4B WILD-TYPE                                          25
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  SEMA4B MUTATED                                        1
  SEMA4B WILD-TYPE                                      7
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  SEMA4B MUTATED                                                 0
  SEMA4B WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  SEMA4B MUTATED                1                   2
  SEMA4B WILD-TYPE             36                  91
D25V18, multiclass
                                                 clus
vv                                                SEMA4B MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               1
  LIFELONG NON-SMOKER                                          2
                                                 clus
vv                                                SEMA4B WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                36
  LIFELONG NON-SMOKER                                           91
[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"
D25V19, continuous
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               1               51 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ       TCGA-C5-A1BL 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M7       TCGA-C5-A1ME       TCGA-C5-A1MF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CL       TCGA-C5-A7CO 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DR-A0ZM       TCGA-DS-A5RQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A556       TCGA-EK-A2RA       TCGA-EX-A1H5       TCGA-FU-A2QG 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ       TCGA-FU-A3TX 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  SEMA4B MUTATED             2        3             0        0        0
  SEMA4B WILD-TYPE          18       51            12        1        7
D25V21, multiclass
               clus
vv              SEMA4B MUTATED SEMA4B WILD-TYPE
  COMBINATION                2               18
  EXTERNAL                   3               51
  EXTERNAL BEAM              0               12
  IMPLANTS                   0                1
  INTERNAL                   0                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"
D25V22, binary
                  cls
clus                0  1
  SEMA4B MUTATED    2  0
  SEMA4B WILD-TYPE 24  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      2    0
  SEMA4B WILD-TYPE   24    3
                         clus
vv                        SEMA4B MUTATED SEMA4B WILD-TYPE
  COMPLETED AS PLANNED                 2               24
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  SEMA4B MUTATED                    1                0                   1
  SEMA4B WILD-TYPE                  1                2                  19
                  vv
clus               REGIONAL SITE
  SEMA4B MUTATED               0
  SEMA4B WILD-TYPE             4
D25V23, multiclass
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               2               26 
      TCGA-C5-A0TN       TCGA-C5-A2LZ       TCGA-C5-A7CK       TCGA-C5-A7CL 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-C5-A7UH 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DS-A7WF       TCGA-EA-A43B 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A5FO       TCGA-EX-A3L1       TCGA-FU-A23L       TCGA-FU-A3HY 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3HZ       TCGA-HM-A3JJ       TCGA-HM-A4S6       TCGA-IR-A3LF 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VG       TCGA-JX-A3Q0       TCGA-JX-A5QV 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-R2-A69V       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V24, binary
                  cls
clus                0  1
  SEMA4B MUTATED    0  0
  SEMA4B WILD-TYPE 16  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      0    0
  SEMA4B WILD-TYPE   16    4
D25V25, continuous
D25V26, continuous
D25V27, continuous
D25V28, continuous
D25V29, continuous
D25V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  SEMA4B MUTATED                                     0
  SEMA4B WILD-TYPE                                   2
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  SEMA4B MUTATED                                     1                       2
  SEMA4B WILD-TYPE                                   6                      26
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  SEMA4B MUTATED                         0                       0
  SEMA4B WILD-TYPE                       1                       6
D25V31, multiclass
                                     clus
vv                                    SEMA4B MUTATED SEMA4B WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT              0                2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT              1                6
  OTHER LOCATION, SPECIFY                          2               26
  POSITIVE BLADDER MARGIN                          0                1
  POSITIVE VAGINAL MARGIN                          0                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)
  SEMA4B MUTATED                                               0
  SEMA4B WILD-TYPE                                             2
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  SEMA4B MUTATED                                                0
  SEMA4B WILD-TYPE                                             10
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  SEMA4B MUTATED                                                                                   4
  SEMA4B WILD-TYPE                                                                                56
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  SEMA4B MUTATED                                                                                              0
  SEMA4B WILD-TYPE                                                                                           88
D25V32, multiclass
                                                                                              clus
vv                                                                                             SEMA4B 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                                                                                             SEMA4B WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               2
  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"
D25V33, binary
                  cls
clus                0  1
  SEMA4B MUTATED    1  1
  SEMA4B WILD-TYPE 62 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      1    1
  SEMA4B WILD-TYPE   62   66
         clus
vv        SEMA4B MUTATED SEMA4B WILD-TYPE
  ABSENT               1               62
  PRESENT              1               66
[1] 2 2
[1] FALSE
D25V34, continuous
D25V35, continuous
D25V36, binary
                  cls
clus                0  1
  SEMA4B MUTATED    3  2
  SEMA4B WILD-TYPE 36 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      3    2
  SEMA4B WILD-TYPE   36   84
                                          clus
vv                                         SEMA4B MUTATED SEMA4B WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  3               36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              2               84
[1] 2 2
[1] FALSE
D25V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  SEMA4B MUTATED              0           0          1
  SEMA4B WILD-TYPE            8          43         45
D25V38, multiclass
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               1               96 
      TCGA-C5-A1BI       TCGA-C5-A1BL       TCGA-C5-A1BN       TCGA-C5-A1M6 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1M7       TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MN       TCGA-C5-A2LT       TCGA-C5-A2LV 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A2M1       TCGA-C5-A2M2 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7UH 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KM       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-DS-A7WF       TCGA-DS-A7WH 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DS-A7WI       TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A3HR       TCGA-EA-A3HT       TCGA-EA-A3HU       TCGA-EA-A3QD 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A3QE       TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A43B 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A44S       TCGA-EA-A4BA       TCGA-EA-A50E       TCGA-EA-A556 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EA-A5O9       TCGA-EA-A5ZE       TCGA-EA-A5ZF       TCGA-EK-A2R7 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EK-A3GK       TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EX-A69L       TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3EO 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A57G 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-FU-A770       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-JW-A5VG       TCGA-JW-A5VI       TCGA-JW-A5VJ       TCGA-JW-A5VK 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-JW-A69B       TCGA-JX-A3PZ       TCGA-JX-A3Q0       TCGA-JX-A3Q8 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-JX-A5QV       TCGA-LP-A5U2       TCGA-LP-A5U3       TCGA-LP-A7HU 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-Q1-A5R1       TCGA-Q1-A5R2       TCGA-Q1-A5R3       TCGA-Q1-A6DV 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-Q1-A73P       TCGA-Q1-A73S       TCGA-UC-A7PD       TCGA-WL-A834 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V39, continuous
D25V40, binary
                  cls
clus                0  1
  SEMA4B MUTATED    2  1
  SEMA4B WILD-TYPE 86 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA4B MUTATED      2    1
  SEMA4B WILD-TYPE   86   15
         clus
vv        SEMA4B MUTATED SEMA4B WILD-TYPE
  ABSENT               2               86
  PRESENT              1               15
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  SEMA4B MUTATED             0         1     0
  SEMA4B WILD-TYPE           2        15     1
D25V41, multiclass
[1] "Remove cluster labels:" "SEMA4B MUTATED"        
clus
  SEMA4B MUTATED SEMA4B WILD-TYPE 
               1               18 
      TCGA-C5-A1BI       TCGA-C5-A1BN       TCGA-C5-A1M9       TCGA-C5-A1MH 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-C5-A1MQ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A3HD 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-DR-A0ZM       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EK-A2H0 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
      TCGA-EK-A2H1       TCGA-HM-A3JJ 
"SEMA4B WILD-TYPE" "SEMA4B WILD-TYPE" 
D25V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  SEMA4B MUTATED      0   1    1    2  0   0    0    0   0  0   0  0  1
  SEMA4B WILD-TYPE    1  20   59   20  4   7    6   10  13  1   2  2  8
D25V43, multiclass
      clus
vv     SEMA4B MUTATED SEMA4B WILD-TYPE
  T1A1              0                1
  T1B               1               20
  T1B1              1               59
  T1B2              2               20
  T2                0                4
  T2A               0                7
  T2A1              0                6
  T2A2              0               10
  T2B               0               13
  T3                0                1
  T3B               0                2
  T4                0                2
  TX                1                8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V44, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  SEMA4B MUTATED         0        0         0         0        1         1
  SEMA4B WILD-TYPE       4        1         1         1       27        52
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  SEMA4B MUTATED           3        0         0          0          0         0
  SEMA4B WILD-TYPE        26        4         6          5          7        14
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  SEMA4B MUTATED           0          1         0         0
  SEMA4B WILD-TYPE         1         28         2         5
D25V45, multiclass
            clus
vv           SEMA4B MUTATED SEMA4B 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              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(26) Variable = ARHGAP4 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  ARHGAP4 MUTATED     3   2
  ARHGAP4 WILD-TYPE 147  38
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                5               185 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                38 
$`ARHGAP4 MUTATED`
TCGA-C5-A7CL TCGA-EK-A2R8 TCGA-EK-A3GK TCGA-IR-A3LK TCGA-JX-A3Q0 
       15.48         1.45         0.10        29.85       195.85 

$`ARHGAP4 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-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-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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.59         0.59         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       21.44        20.48        15.58        28.37         8.28        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       30.31         7.99        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.35        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
             0.10              0.03 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
           195.85            210.67 
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
            15.48             19.79 
[1] "0.1 - 195.8 (15.5)" "0.0 - 210.7 (19.8)"
[1] "hr=" "1.9"
D26V2, continuous
                   vv
clus                 T1  T2 T3+T4
  ARHGAP4 MUTATED     4   0     1
  ARHGAP4 WILD-TYPE 100  40     4
D26V3, multiclass
       clus
vv      ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  T1                  4               100
  T2                  0                40
  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"
D26V4, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    4  1
  ARHGAP4 WILD-TYPE 91 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      4    1
  ARHGAP4 WILD-TYPE   91   43
   clus
vv  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  0               4                91
  1               1                43
[1] 2 2
[1] FALSE
D26V5, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    3  0
  ARHGAP4 WILD-TYPE 76  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      3    0
  ARHGAP4 WILD-TYPE   76    4
   clus
vv  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  0               3                76
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ARHGAP4 MUTATED               0                                5
  ARHGAP4 WILD-TYPE             4                              153
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  ARHGAP4 MUTATED                                               0
  ARHGAP4 WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  ARHGAP4 MUTATED                                     1
  ARHGAP4 WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  ARHGAP4 MUTATED                                           0
  ARHGAP4 WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  ARHGAP4 MUTATED                                              0
  ARHGAP4 WILD-TYPE                                            3
D26V6, multiclass
                                               clus
vv                                              ARHGAP4 MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            5
  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                                              ARHGAP4 WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  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"
D26V7, binary
                   cls
clus                  0   1
  ARHGAP4 MUTATED     0   6
  ARHGAP4 WILD-TYPE  32 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      0    6
  ARHGAP4 WILD-TYPE   32  156
     clus
vv    ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  NO                0                32
  YES               6               156
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                55 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-DG-A2KK        TCGA-DG-A2KL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
D26V9, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2               119 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-BI-A20A        TCGA-C5-A0TN 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BK        TCGA-C5-A1BL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A1MQ        TCGA-C5-A2LS 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7UC        TCGA-C5-A7UE        TCGA-DG-A2KH 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DG-A2KJ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DG-A2KM 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A1OA        TCGA-DS-A3LQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A3HT        TCGA-EA-A3HU        TCGA-EA-A3QD        TCGA-EA-A3Y4 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A43B        TCGA-EA-A44S 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5FO 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A6QX        TCGA-EK-A2RA        TCGA-EK-A2RO 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1        TCGA-EX-A69L 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-JX-A3PZ        TCGA-JX-A3Q8        TCGA-JX-A5QV        TCGA-LP-A4AX 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-LP-A5U2        TCGA-LP-A7HU        TCGA-MU-A51Y        TCGA-MU-A5YI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MY-A5BD        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP4 MUTATED                                  0     1
  ARHGAP4 WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  ARHGAP4 MUTATED                           1
  ARHGAP4 WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP4 MUTATED                                           0     4
  ARHGAP4 WILD-TYPE                                         1   134
D26V10, multiclass
                                           clus
vv                                          ARHGAP4 MUTATED ARHGAP4 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                                                   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"
D26V11, binary
                   cls
clus                  0   1
  ARHGAP4 MUTATED     0   4
  ARHGAP4 WILD-TYPE  14 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      0    4
  ARHGAP4 WILD-TYPE   14  130
                        clus
vv                       ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO               4               130
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    1  1
  ARHGAP4 WILD-TYPE 96 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      1    1
  ARHGAP4 WILD-TYPE   96   30
            clus
vv           ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  TUMOR FREE               1                96
  WITH TUMOR               1                30
[1] 2 2
[1] FALSE
                   vv
clus                CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  ARHGAP4 MUTATED        0      0       0             5       1
  ARHGAP4 WILD-TYPE      5     10       6           154      13
D26V14, multiclass
               clus
vv              ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CANADA                      0                 5
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES               5               154
  VIETNAM                     1                13
[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                G1 G2 G3 G4 GX
  ARHGAP4 MUTATED    0  3  3  0  0
  ARHGAP4 WILD-TYPE 14 85 79  1  8
D26V15, multiclass
    clus
vv   ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  G1               0                14
  G2               3                85
  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"
D26V16, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                1                28 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A2M2 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DG-A2KK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EK-A2RA        TCGA-EX-A69M        TCGA-FU-A2QG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK        TCGA-HM-A4S6 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-MU-A5YI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73S        TCGA-RA-A741        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
D26V17, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                55 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-DG-A2KK        TCGA-DG-A2KL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  ARHGAP4 MUTATED                                             1
  ARHGAP4 WILD-TYPE                                          25
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  ARHGAP4 MUTATED                                        0
  ARHGAP4 WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  ARHGAP4 MUTATED                                                 0
  ARHGAP4 WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  ARHGAP4 MUTATED                1                   2
  ARHGAP4 WILD-TYPE             36                  91
D26V18, multiclass
                                                 clus
vv                                                ARHGAP4 MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                1
  LIFELONG NON-SMOKER                                           2
                                                 clus
vv                                                ARHGAP4 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 36
  LIFELONG NON-SMOKER                                            91
[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"
D26V19, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                50 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CO 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-DG-A2KK        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A556        TCGA-EK-A2RA        TCGA-EX-A1H5        TCGA-FU-A2QG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3TX 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
D26V20, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                80 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1M6        TCGA-C5-A1M8 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1ML        TCGA-C5-A1MQ        TCGA-C5-A2LT        TCGA-C5-A2LX 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A2LZ        TCGA-C5-A3HD        TCGA-C5-A3HF 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DG-A2KJ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DG-A2KM 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VN        TCGA-DS-A1OA 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WH        TCGA-DS-A7WI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3Y4        TCGA-EA-A43B        TCGA-EA-A44S 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A5FO        TCGA-EA-A5O9        TCGA-EK-A2H0 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A449        TCGA-FU-A23L        TCGA-FU-A3HY 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3HZ        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VH        TCGA-JW-A5VI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-JX-A5QV        TCGA-LP-A4AU        TCGA-LP-A4AX        TCGA-LP-A7HU 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MY-A5BD        TCGA-MY-A5BF        TCGA-Q1-A5R2 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A5R3        TCGA-Q1-A6DW        TCGA-Q1-A73O        TCGA-Q1-A73Q 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  ARHGAP4 MUTATED             0        2             0        0        1
  ARHGAP4 WILD-TYPE          20       52            12        1        6
D26V21, multiclass
               clus
vv              ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  COMBINATION                 0                20
  EXTERNAL                    2                52
  EXTERNAL BEAM               0                12
  IMPLANTS                    0                 1
  INTERNAL                    1                 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"
D26V22, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    0  0
  ARHGAP4 WILD-TYPE 26  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      0    0
  ARHGAP4 WILD-TYPE   26    3
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  ARHGAP4 MUTATED                    0                0                   1
  ARHGAP4 WILD-TYPE                  2                2                  19
                   vv
clus                REGIONAL SITE
  ARHGAP4 MUTATED               1
  ARHGAP4 WILD-TYPE             3
D26V23, multiclass
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2                26 
       TCGA-C5-A0TN        TCGA-C5-A1BF        TCGA-C5-A1BQ        TCGA-C5-A2LZ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-C5-A7UE 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-DG-A2KL        TCGA-DS-A7WF 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A5FO        TCGA-EX-A3L1        TCGA-FU-A23L 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-HM-A3JJ        TCGA-HM-A4S6 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-JW-A5VG        TCGA-JX-A5QV 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-R2-A69V        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
D26V24, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    1  1
  ARHGAP4 WILD-TYPE 15  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      1    1
  ARHGAP4 WILD-TYPE   15    3
     clus
vv    ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CGY               1                15
  GY                1                 3
[1] 2 2
[1] FALSE
D26V25, continuous
D26V26, continuous
D26V27, continuous
D26V28, continuous
D26V29, continuous
D26V30, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ARHGAP4 MUTATED                                     0
  ARHGAP4 WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ARHGAP4 MUTATED                                     1                       0
  ARHGAP4 WILD-TYPE                                   6                      28
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ARHGAP4 MUTATED                         0                       0
  ARHGAP4 WILD-TYPE                       1                       6
D26V31, multiclass
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                1                43 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BK 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MJ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-C5-A1MQ        TCGA-C5-A2LS        TCGA-C5-A2LT 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2M1        TCGA-C5-A3HE 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7UC 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DG-A2KL        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A1OA        TCGA-DS-A3LQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A50E        TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6        TCGA-IR-A3LH 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-UC-A7PD        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  ARHGAP4 MUTATED                                               0
  ARHGAP4 WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  ARHGAP4 MUTATED                                                0
  ARHGAP4 WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  ARHGAP4 MUTATED                                                                                   2
  ARHGAP4 WILD-TYPE                                                                                58
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ARHGAP4 MUTATED                                                                                              1
  ARHGAP4 WILD-TYPE                                                                                           87
D26V32, multiclass
                                                                                              clus
vv                                                                                             ARHGAP4 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                                                                                             ARHGAP4 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  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"
D26V33, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    1  1
  ARHGAP4 WILD-TYPE 62 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      1    1
  ARHGAP4 WILD-TYPE   62   66
         clus
vv        ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  ABSENT                1                62
  PRESENT               1                66
[1] 2 2
[1] FALSE
D26V34, continuous
[1] "Remove cluster labels:" "ARHGAP4 MUTATED"       
clus
  ARHGAP4 MUTATED ARHGAP4 WILD-TYPE 
                2               119 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-BI-A20A        TCGA-C5-A0TN 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BK        TCGA-C5-A1BL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A1MQ        TCGA-C5-A2LS 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7UC        TCGA-C5-A7UE        TCGA-DG-A2KH 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DG-A2KJ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DG-A2KM 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A1OA        TCGA-DS-A3LQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A3HT        TCGA-EA-A3HU        TCGA-EA-A3QD        TCGA-EA-A3Y4 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A43B        TCGA-EA-A44S 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5FO 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A6QX        TCGA-EK-A2RA        TCGA-EK-A2RO 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1        TCGA-EX-A69L 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LL 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-JX-A3PZ        TCGA-JX-A3Q8        TCGA-JX-A5QV        TCGA-LP-A4AX 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-LP-A5U2        TCGA-LP-A7HU        TCGA-MU-A51Y        TCGA-MU-A5YI 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-MY-A5BD        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-Q1-A73S        TCGA-R2-A69V        TCGA-RA-A741 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF        TCGA-WL-A834 
"ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" "ARHGAP4 WILD-TYPE" 
D26V35, continuous
D26V36, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    3  0
  ARHGAP4 WILD-TYPE 36 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      3    0
  ARHGAP4 WILD-TYPE   36   86
                                          clus
vv                                         ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               0                86
[1] 2 2
[1] FALSE
D26V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  ARHGAP4 MUTATED              1           0          2
  ARHGAP4 WILD-TYPE            7          43         44
D26V38, multiclass
              clus
vv             ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                0                43
  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"
D26V39, continuous
D26V40, binary
                   cls
clus                 0  1
  ARHGAP4 MUTATED    3  0
  ARHGAP4 WILD-TYPE 85 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP4 MUTATED      3    0
  ARHGAP4 WILD-TYPE   85   16
         clus
vv        ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  ABSENT                3                85
  PRESENT               0                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  ARHGAP4 MUTATED             0         0     0
  ARHGAP4 WILD-TYPE           2        16     1
D26V41, multiclass
D26V42, continuous
                   vv
clus                T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  ARHGAP4 MUTATED      0   1    1    2  0   0    0    0   0  1   0  0  0
  ARHGAP4 WILD-TYPE    1  20   59   20  4   7    6   10  13  0   2  2  9
D26V43, multiclass
      clus
vv     ARHGAP4 MUTATED ARHGAP4 WILD-TYPE
  T1A1               0                 1
  T1B                1                20
  T1B1               1                59
  T1B2               2                20
  T2                 0                 4
  T2A                0                 7
  T2A1               0                 6
  T2A2               0                10
  T2B                0                13
  T3                 1                 0
  T3B                0                 2
  T4                 0                 2
  TX                 0                 9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V44, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  ARHGAP4 MUTATED         0        0         0         0        1         1
  ARHGAP4 WILD-TYPE       4        1         1         1       27        52
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  ARHGAP4 MUTATED           2        0         0          0          0
  ARHGAP4 WILD-TYPE        27        4         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  ARHGAP4 MUTATED           0         1          1         0         0
  ARHGAP4 WILD-TYPE        14         0         28         2         5
D26V45, multiclass
            clus
vv           ARHGAP4 MUTATED ARHGAP4 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                2                27
  STAGE II                 0                 4
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                0                14
  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(27) Variable = POU2F1 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  POU2F1 MUTATED     2   1
  POU2F1 WILD-TYPE 148  39
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               3              187 
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               1               39 
$`POU2F1 MUTATED`
TCGA-C5-A1BJ TCGA-DR-A0ZM TCGA-IR-A3LK 
      144.16        58.88        29.85 

$`POU2F1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        87.75        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         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       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        36.36        27.42         3.29 
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       195.85        30.31         7.99        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        13.87        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  POU2F1 MUTATED POU2F1 WILD-TYPE 
           29.85             0.03 
  POU2F1 MUTATED POU2F1 WILD-TYPE 
          144.16           210.67 
  POU2F1 MUTATED POU2F1 WILD-TYPE 
           58.88            19.36 
[1] "29.9 - 144.2 (58.9)" "0.0 - 210.7 (19.4)" 
[1] "hr=" "1.4"
D27V2, continuous
                  vv
clus                T1  T2 T3+T4
  POU2F1 MUTATED     1   1     0
  POU2F1 WILD-TYPE 103  39     5
D27V3, multiclass
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              147 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BK       TCGA-C5-A1BM       TCGA-C5-A1M5 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M7       TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MP 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MQ       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A2M1       TCGA-C5-A3HE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7CJ       TCGA-C5-A7UC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KH       TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KM       TCGA-DR-A0ZL       TCGA-DS-A0VK       TCGA-DS-A0VL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HT       TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3Y4       TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A439 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A43B       TCGA-EA-A44S       TCGA-EA-A4BA       TCGA-EA-A50E 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A556       TCGA-EA-A5FO       TCGA-EA-A5O9       TCGA-EA-A5ZD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5ZE       TCGA-EA-A5ZF       TCGA-EA-A6QX       TCGA-EA-A78R 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2IP       TCGA-EK-A2R7       TCGA-EK-A2R8       TCGA-EK-A2R9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EK-A2RD       TCGA-EK-A2RE       TCGA-EK-A2RJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RK       TCGA-EK-A2RL       TCGA-EK-A2RN       TCGA-EK-A3GJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A3GK       TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A449       TCGA-EX-A69L       TCGA-EX-A69M       TCGA-FU-A23K 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A23L       TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3HZ       TCGA-FU-A3NI       TCGA-FU-A3TQ       TCGA-FU-A3TX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A40J       TCGA-FU-A57G 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A5XV       TCGA-FU-A770       TCGA-HG-A2PA       TCGA-HM-A3JJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LA       TCGA-IR-A3LB       TCGA-IR-A3LC       TCGA-IR-A3LF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LL       TCGA-JW-A5VG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VH       TCGA-JW-A5VI       TCGA-JW-A5VJ       TCGA-JW-A5VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VL       TCGA-JW-A69B       TCGA-JW-A852       TCGA-JX-A3PZ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3Q0       TCGA-JX-A3Q8       TCGA-JX-A5QV       TCGA-LP-A4AU 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A4AV       TCGA-LP-A4AW       TCGA-LP-A4AX       TCGA-LP-A5U2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A5U3       TCGA-LP-A7HU       TCGA-MU-A51Y       TCGA-MU-A5YI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MY-A5BD       TCGA-MY-A5BE       TCGA-MY-A5BF       TCGA-Q1-A5R1 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A6DV       TCGA-Q1-A73P       TCGA-Q1-A73S       TCGA-R2-A69V 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-UC-A7PF       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V4, binary
                  cls
clus                0  1
  POU2F1 MUTATED    2  0
  POU2F1 WILD-TYPE 93 44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      2    0
  POU2F1 WILD-TYPE   93   44
   clus
vv  POU2F1 MUTATED POU2F1 WILD-TYPE
  0              2               93
  1              0               44
[1] 2 2
[1] FALSE
D27V5, binary
                  cls
clus                0  1
  POU2F1 MUTATED    2  0
  POU2F1 WILD-TYPE 77  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      2    0
  POU2F1 WILD-TYPE   77    4
   clus
vv  POU2F1 MUTATED POU2F1 WILD-TYPE
  0              2               77
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  POU2F1 MUTATED               0                                3
  POU2F1 WILD-TYPE             4                              155
                  vv
clus               ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  POU2F1 MUTATED                                               0
  POU2F1 WILD-TYPE                                             5
                  vv
clus               ENDOCERVICAL TYPE OF ADENOCARCINOMA
  POU2F1 MUTATED                                     0
  POU2F1 WILD-TYPE                                  22
                  vv
clus               ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  POU2F1 MUTATED                                           0
  POU2F1 WILD-TYPE                                         2
                  vv
clus               MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  POU2F1 MUTATED                                              0
  POU2F1 WILD-TYPE                                            3
D27V6, multiclass
                                               clus
vv                                              POU2F1 MUTATED POU2F1 WILD-TYPE
  ADENOSQUAMOUS                                              0                4
  CERVICAL SQUAMOUS CELL CARCINOMA                           3              155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE              0                5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        0               22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D27V7, binary
                  cls
clus                 0   1
  POU2F1 MUTATED     2   1
  POU2F1 WILD-TYPE  30 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      2    1
  POU2F1 WILD-TYPE   30  161
     clus
vv    POU2F1 MUTATED POU2F1 WILD-TYPE
  NO               2               30
  YES              1              161
[1] 2 2
[1] FALSE
D27V8, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V9, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              119 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BK       TCGA-C5-A1BL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MJ       TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2M1       TCGA-C5-A3HF       TCGA-C5-A3HL       TCGA-C5-A7CG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7UC       TCGA-C5-A7UE       TCGA-DG-A2KH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DG-A2KM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DR-A0ZL       TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-DS-A5RQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI       TCGA-EA-A1QS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR       TCGA-EA-A3HT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3Y4       TCGA-EA-A410 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A411       TCGA-EA-A43B       TCGA-EA-A44S       TCGA-EA-A4BA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A50E       TCGA-EA-A556       TCGA-EA-A5FO       TCGA-EA-A5O9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A6QX       TCGA-EK-A2RA       TCGA-EK-A2RO       TCGA-EK-A3GK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1       TCGA-EX-A69L 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A23K       TCGA-FU-A23L       TCGA-FU-A2QG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3NI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3TX       TCGA-FU-A3WB       TCGA-FU-A3YQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A40J       TCGA-FU-A57G       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HG-A2PA       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB       TCGA-IR-A3LC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3PZ       TCGA-JX-A3Q8       TCGA-JX-A5QV       TCGA-LP-A4AX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A5U2       TCGA-LP-A7HU       TCGA-MU-A51Y       TCGA-MU-A5YI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MY-A5BD       TCGA-MY-A5BF       TCGA-Q1-A5R1       TCGA-Q1-A6DV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A73P       TCGA-Q1-A73S       TCGA-R2-A69V       TCGA-RA-A741 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-UC-A7PF       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POU2F1 MUTATED                                  0     0
  POU2F1 WILD-TYPE                                8    19
                  vv
clus               BLACK OR AFRICAN AMERICAN
  POU2F1 MUTATED                           0
  POU2F1 WILD-TYPE                        16
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POU2F1 MUTATED                                           0     3
  POU2F1 WILD-TYPE                                         1   135
D27V10, multiclass
                                           clus
vv                                          POU2F1 MUTATED POU2F1 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                                                  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"
D27V11, binary
                  cls
clus                 0   1
  POU2F1 MUTATED     0   1
  POU2F1 WILD-TYPE  14 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      0    1
  POU2F1 WILD-TYPE   14  133
                        clus
vv                       POU2F1 MUTATED POU2F1 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              1              133
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                  cls
clus                0  1
  POU2F1 MUTATED    2  1
  POU2F1 WILD-TYPE 95 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      2    1
  POU2F1 WILD-TYPE   95   30
            clus
vv           POU2F1 MUTATED POU2F1 WILD-TYPE
  TUMOR FREE              2               95
  WITH TUMOR              1               30
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  POU2F1 MUTATED        0      0       0             3       0
  POU2F1 WILD-TYPE      5     10       6           156      14
D27V14, multiclass
               clus
vv              POU2F1 MUTATED POU2F1 WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    0                6
  UNITED STATES              3              156
  VIETNAM                    0               14
[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               G1 G2 G3 G4 GX
  POU2F1 MUTATED    0  2  1  0  0
  POU2F1 WILD-TYPE 14 86 81  1  8
D27V15, multiclass
    clus
vv   POU2F1 MUTATED POU2F1 WILD-TYPE
  G1              0               14
  G2              2               86
  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"
D27V16, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               1               28 
      TCGA-BI-A0VR       TCGA-C5-A1BL       TCGA-C5-A1BQ       TCGA-C5-A1ME 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A2M2       TCGA-C5-A3HD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CM       TCGA-C5-A7CO       TCGA-DG-A2KK       TCGA-DS-A3LQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3TX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-IR-A3L7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LB       TCGA-IR-A3LH       TCGA-JX-A3Q0       TCGA-MU-A5YI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73S       TCGA-RA-A741       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V17, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               55 
      TCGA-BI-A0VR       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1ML 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CK       TCGA-C5-A7CL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DG-A2KL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-EA-A556       TCGA-EX-A1H5 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3TQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A4S6       TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MU-A5YI       TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  POU2F1 MUTATED                                             1
  POU2F1 WILD-TYPE                                          25
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  POU2F1 MUTATED                                        0
  POU2F1 WILD-TYPE                                      8
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  POU2F1 MUTATED                                                 0
  POU2F1 WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  POU2F1 MUTATED                1                   1
  POU2F1 WILD-TYPE             36                  92
D27V18, multiclass
                                                 clus
vv                                                POU2F1 MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               1
  LIFELONG NON-SMOKER                                          1
                                                 clus
vv                                                POU2F1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                36
  LIFELONG NON-SMOKER                                           92
[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"
D27V19, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               50 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BL       TCGA-C5-A1BN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME       TCGA-C5-A1MF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LZ       TCGA-C5-A2M2       TCGA-C5-A3HD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HF       TCGA-C5-A7CJ       TCGA-C5-A7CL       TCGA-C5-A7CO 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-DG-A2KK       TCGA-DS-A5RQ       TCGA-EA-A556 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EX-A1H5       TCGA-FU-A2QG       TCGA-FU-A3EO 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3TQ       TCGA-FU-A3TX       TCGA-FU-A3WB 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3YQ       TCGA-FU-A5XV       TCGA-FU-A770       TCGA-HM-A4S6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LB       TCGA-IR-A3LH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VI       TCGA-JW-A5VK       TCGA-JX-A3Q0       TCGA-MU-A5YI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A6DW       TCGA-Q1-A73Q       TCGA-Q1-A73S       TCGA-RA-A741 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  POU2F1 MUTATED             1        1             1        0        0
  POU2F1 WILD-TYPE          19       53            11        1        7
D27V21, multiclass
               clus
vv              POU2F1 MUTATED POU2F1 WILD-TYPE
  COMBINATION                1               19
  EXTERNAL                   1               53
  EXTERNAL BEAM              1               11
  IMPLANTS                   0                1
  INTERNAL                   0                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"
D27V22, binary
                  cls
clus                0  1
  POU2F1 MUTATED    2  0
  POU2F1 WILD-TYPE 24  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      2    0
  POU2F1 WILD-TYPE   24    3
                         clus
vv                        POU2F1 MUTATED POU2F1 WILD-TYPE
  COMPLETED AS PLANNED                 2               24
  TREATMENT NOT COMPLETED              0                3
[1] 2 2
[1] FALSE
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  POU2F1 MUTATED                    0                0                   0
  POU2F1 WILD-TYPE                  2                2                  20
                  vv
clus               REGIONAL SITE
  POU2F1 MUTATED               0
  POU2F1 WILD-TYPE             4
D27V23, multiclass
D27V24, binary
                  cls
clus                0  1
  POU2F1 MUTATED    0  0
  POU2F1 WILD-TYPE 16  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      0    0
  POU2F1 WILD-TYPE   16    4
D27V25, continuous
D27V26, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               99 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BE       TCGA-C5-A1BI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BL       TCGA-C5-A1BM       TCGA-C5-A1BN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1M5       TCGA-C5-A1M6       TCGA-C5-A1M7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1ML       TCGA-C5-A1MN       TCGA-C5-A1MP       TCGA-C5-A1MQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LY       TCGA-C5-A2LZ       TCGA-C5-A2M1       TCGA-C5-A2M2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HE       TCGA-C5-A3HF       TCGA-C5-A3HL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CG       TCGA-C5-A7CH       TCGA-C5-A7CJ       TCGA-C5-A7CK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-C5-A7UH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DR-A0ZL       TCGA-DS-A0VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE       TCGA-EA-A3Y4 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A44S       TCGA-EA-A556 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5O9       TCGA-EX-A449       TCGA-FU-A2QG       TCGA-FU-A3EO 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3TQ       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HG-A2PA       TCGA-HM-A3JK       TCGA-IR-A3L7       TCGA-IR-A3LC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VG       TCGA-JW-A5VH       TCGA-JW-A5VI       TCGA-JW-A5VJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VK       TCGA-JW-A5VL       TCGA-JW-A69B       TCGA-JW-A852 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3PZ       TCGA-JX-A3Q0       TCGA-JX-A3Q8       TCGA-JX-A5QV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-UC-A7PF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V27, continuous
D27V28, continuous
D27V29, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              107 
      TCGA-BI-A0VS       TCGA-C5-A0TN       TCGA-C5-A1BE       TCGA-C5-A1BI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BL       TCGA-C5-A1BM       TCGA-C5-A1BN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1M5       TCGA-C5-A1M6       TCGA-C5-A1M7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1ML       TCGA-C5-A1MN       TCGA-C5-A1MP       TCGA-C5-A1MQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LY       TCGA-C5-A2LZ       TCGA-C5-A2M1       TCGA-C5-A2M2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HE       TCGA-C5-A3HF       TCGA-C5-A3HL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CG       TCGA-C5-A7CH       TCGA-C5-A7CJ       TCGA-C5-A7CK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-C5-A7UH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DR-A0ZL       TCGA-DS-A0VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HT       TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3Y4       TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A44S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A4BA       TCGA-EA-A556       TCGA-EA-A5O9       TCGA-EA-A6QX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RN       TCGA-EX-A1H6       TCGA-EX-A449       TCGA-FU-A2QG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3TQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A770       TCGA-HG-A2PA       TCGA-HM-A3JJ       TCGA-HM-A3JK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3L7       TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LI       TCGA-IR-A3LL       TCGA-JW-A5VG       TCGA-JW-A5VH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VI       TCGA-JW-A5VJ       TCGA-JW-A5VK       TCGA-JW-A5VL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A69B       TCGA-JW-A852       TCGA-JX-A3PZ       TCGA-JX-A3Q0 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3Q8       TCGA-JX-A5QV       TCGA-LP-A5U2       TCGA-MU-A51Y 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-RA-A741       TCGA-UC-A7PD       TCGA-UC-A7PF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V30, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              101 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BE       TCGA-C5-A1BI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BL       TCGA-C5-A1BM       TCGA-C5-A1BN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1M5       TCGA-C5-A1M6       TCGA-C5-A1M7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1ML       TCGA-C5-A1MN       TCGA-C5-A1MP       TCGA-C5-A1MQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LS       TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LY       TCGA-C5-A2LZ       TCGA-C5-A2M1       TCGA-C5-A2M2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HE       TCGA-C5-A3HF       TCGA-C5-A3HL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CG       TCGA-C5-A7CH       TCGA-C5-A7CJ       TCGA-C5-A7CK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CL       TCGA-C5-A7CO       TCGA-C5-A7UE       TCGA-C5-A7UH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DR-A0ZL       TCGA-DS-A0VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE       TCGA-EA-A3Y4 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A44S       TCGA-EA-A556 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5O9       TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3EO 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3TQ       TCGA-FU-A5XV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A770       TCGA-HG-A2PA       TCGA-HM-A3JK       TCGA-IR-A3L7 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LL       TCGA-JW-A5VG       TCGA-JW-A5VH       TCGA-JW-A5VI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VJ       TCGA-JW-A5VK       TCGA-JW-A5VL       TCGA-JW-A69B 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A852       TCGA-JX-A3PZ       TCGA-JX-A3Q0       TCGA-JX-A3Q8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A5QV       TCGA-Q1-A73Q       TCGA-RA-A741       TCGA-UC-A7PD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PF 
"POU2F1 WILD-TYPE" 
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  POU2F1 MUTATED                                     0
  POU2F1 WILD-TYPE                                   2
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  POU2F1 MUTATED                                     1                       1
  POU2F1 WILD-TYPE                                   6                      27
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  POU2F1 MUTATED                         0                       0
  POU2F1 WILD-TYPE                       1                       6
D27V31, multiclass
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               42 
      TCGA-BI-A20A       TCGA-C5-A0TN       TCGA-C5-A1BE       TCGA-C5-A1BK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS       TCGA-C5-A2LT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2M1       TCGA-C5-A3HE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7CJ       TCGA-C5-A7UC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KL       TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EA-A50E 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RN       TCGA-EK-A2RO       TCGA-EX-A1H5       TCGA-EX-A449 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-HM-A4S6       TCGA-IR-A3LH       TCGA-IR-A3LI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  POU2F1 MUTATED                                               0
  POU2F1 WILD-TYPE                                             2
                  vv
clus               PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  POU2F1 MUTATED                                                0
  POU2F1 WILD-TYPE                                             10
                  vv
clus               POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  POU2F1 MUTATED                                                                                   2
  POU2F1 WILD-TYPE                                                                                58
                  vv
clus               PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  POU2F1 MUTATED                                                                                              1
  POU2F1 WILD-TYPE                                                                                           87
D27V32, multiclass
                                                                                              clus
vv                                                                                             POU2F1 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                                                                                             POU2F1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               2
  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"
D27V33, binary
                  cls
clus                0  1
  POU2F1 MUTATED    0  1
  POU2F1 WILD-TYPE 63 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      0    1
  POU2F1 WILD-TYPE   63   66
         clus
vv        POU2F1 MUTATED POU2F1 WILD-TYPE
  ABSENT               0               63
  PRESENT              1               66
[1] 2 2
[1] FALSE
D27V34, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              119 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BK       TCGA-C5-A1BL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MJ       TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2M1       TCGA-C5-A3HF       TCGA-C5-A3HL       TCGA-C5-A7CG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7UC       TCGA-C5-A7UE       TCGA-DG-A2KH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DG-A2KM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DR-A0ZL       TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-DS-A5RQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI       TCGA-EA-A1QS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR       TCGA-EA-A3HT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3Y4       TCGA-EA-A410 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A411       TCGA-EA-A43B       TCGA-EA-A44S       TCGA-EA-A4BA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A50E       TCGA-EA-A556       TCGA-EA-A5FO       TCGA-EA-A5O9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A6QX       TCGA-EK-A2RA       TCGA-EK-A2RO       TCGA-EK-A3GK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1       TCGA-EX-A69L 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A23K       TCGA-FU-A23L       TCGA-FU-A2QG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3NI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3TX       TCGA-FU-A3WB       TCGA-FU-A3YQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A40J       TCGA-FU-A57G       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HG-A2PA       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB       TCGA-IR-A3LC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-IR-A3LL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3PZ       TCGA-JX-A3Q8       TCGA-JX-A5QV       TCGA-LP-A4AX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A5U2       TCGA-LP-A7HU       TCGA-MU-A51Y       TCGA-MU-A5YI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MY-A5BD       TCGA-MY-A5BF       TCGA-Q1-A5R1       TCGA-Q1-A6DV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A73P       TCGA-Q1-A73S       TCGA-R2-A69V       TCGA-RA-A741 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PD       TCGA-UC-A7PF       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V35, continuous
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              138 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BK       TCGA-C5-A1BL 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BM       TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MJ       TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LT       TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2M1       TCGA-C5-A3HF       TCGA-C5-A3HL       TCGA-C5-A7CG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7CJ       TCGA-C5-A7UC       TCGA-C5-A7UE       TCGA-DG-A2KH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KJ       TCGA-DG-A2KK       TCGA-DG-A2KL       TCGA-DG-A2KM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DR-A0ZL       TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VN       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-DS-A5RQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI       TCGA-EA-A1QS 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR       TCGA-EA-A3HT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE       TCGA-EA-A3Y4 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A43B       TCGA-EA-A44S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A4BA       TCGA-EA-A50E       TCGA-EA-A556       TCGA-EA-A5FO 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5O9       TCGA-EA-A6QX       TCGA-EK-A2GZ       TCGA-EK-A2IP 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2PK       TCGA-EK-A2R7       TCGA-EK-A2R8       TCGA-EK-A2R9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EK-A2RC       TCGA-EK-A2RD       TCGA-EK-A2RE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RJ       TCGA-EK-A2RK       TCGA-EK-A2RL       TCGA-EK-A2RM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RN       TCGA-EK-A2RO       TCGA-EK-A3GJ       TCGA-EK-A3GK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1       TCGA-EX-A69L 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A23K       TCGA-FU-A23L       TCGA-FU-A2QG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3NI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3TX       TCGA-FU-A3WB       TCGA-FU-A3YQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A40J       TCGA-FU-A57G       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HG-A2PA       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LL       TCGA-JX-A3PZ       TCGA-JX-A3Q8       TCGA-JX-A5QV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A4AV       TCGA-LP-A4AW       TCGA-LP-A4AX       TCGA-LP-A5U2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A7HU       TCGA-MU-A51Y       TCGA-MU-A5YI       TCGA-MY-A5BD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MY-A5BF       TCGA-Q1-A5R1       TCGA-Q1-A6DV       TCGA-Q1-A73P 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A73S       TCGA-R2-A69V       TCGA-RA-A741       TCGA-UC-A7PD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-UC-A7PF       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V36, binary
                  cls
clus                0  1
  POU2F1 MUTATED    0  1
  POU2F1 WILD-TYPE 39 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      0    1
  POU2F1 WILD-TYPE   39   85
                                          clus
vv                                         POU2F1 MUTATED POU2F1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  0               39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              1               85
[1] 2 2
[1] FALSE
D27V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  POU2F1 MUTATED              0           1          1
  POU2F1 WILD-TYPE            8          42         45
D27V38, multiclass
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2               95 
      TCGA-C5-A1BI       TCGA-C5-A1BL       TCGA-C5-A1BN       TCGA-C5-A1M6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M7       TCGA-C5-A1M8       TCGA-C5-A1M9       TCGA-C5-A1ME 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MN       TCGA-C5-A2LT       TCGA-C5-A2LV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A2M1       TCGA-C5-A2M2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7UH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7X3       TCGA-DG-A2KM       TCGA-DR-A0ZL       TCGA-DS-A0VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-DS-A7WF       TCGA-DS-A7WH       TCGA-DS-A7WI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ       TCGA-EA-A3HR 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HT       TCGA-EA-A3HU       TCGA-EA-A3QD       TCGA-EA-A3QE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A410       TCGA-EA-A411       TCGA-EA-A43B       TCGA-EA-A44S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A4BA       TCGA-EA-A50E       TCGA-EA-A556       TCGA-EA-A5O9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5ZE       TCGA-EA-A5ZF       TCGA-EK-A2R7       TCGA-EK-A3GK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-EX-A1H6       TCGA-EX-A3L1       TCGA-EX-A69L 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3EO       TCGA-FU-A3HY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3WB       TCGA-FU-A3YQ       TCGA-FU-A57G       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6       TCGA-HM-A6W2 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB       TCGA-IR-A3LC 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI       TCGA-JW-A5VG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VI       TCGA-JW-A5VJ       TCGA-JW-A5VK       TCGA-JW-A69B 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A3PZ       TCGA-JX-A3Q0       TCGA-JX-A3Q8       TCGA-JX-A5QV 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A5U2       TCGA-LP-A5U3       TCGA-LP-A7HU       TCGA-Q1-A5R1 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A5R2       TCGA-Q1-A5R3       TCGA-Q1-A6DV       TCGA-Q1-A73P 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A73S       TCGA-UC-A7PD       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V39, continuous
D27V40, binary
                  cls
clus                0  1
  POU2F1 MUTATED    1  1
  POU2F1 WILD-TYPE 87 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU2F1 MUTATED      1    1
  POU2F1 WILD-TYPE   87   15
         clus
vv        POU2F1 MUTATED POU2F1 WILD-TYPE
  ABSENT               1               87
  PRESENT              1               15
[1] 2 2
[1] FALSE
                  vv
clus               CARBOPLATIN CISPLATIN OTHER
  POU2F1 MUTATED             0         1     0
  POU2F1 WILD-TYPE           2        15     1
D27V41, multiclass
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               1               18 
      TCGA-C5-A1BE       TCGA-C5-A1BI       TCGA-C5-A1BN       TCGA-C5-A1M9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MH       TCGA-C5-A1MI       TCGA-C5-A1MK       TCGA-C5-A1MN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MQ       TCGA-C5-A2LT       TCGA-C5-A2LX       TCGA-C5-A2LY 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HD       TCGA-DS-A1OA       TCGA-DS-A3LQ       TCGA-EK-A2H0 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2H1       TCGA-HM-A3JJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  POU2F1 MUTATED      0   0    0    1  0   0    0    0   1  0   0  0  0
  POU2F1 WILD-TYPE    1  21   60   21  4   7    6   10  12  1   2  2  9
D27V43, multiclass
[1] "Remove cluster labels:" "POU2F1 MUTATED"        
clus
  POU2F1 MUTATED POU2F1 WILD-TYPE 
               2              156 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BK       TCGA-C5-A1BM 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1M7       TCGA-C5-A1M8       TCGA-C5-A1M9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A1MP       TCGA-C5-A1MQ       TCGA-C5-A2LS       TCGA-C5-A2LT 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A2LV       TCGA-C5-A2LX       TCGA-C5-A2LY       TCGA-C5-A2M1 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A3HE       TCGA-C5-A3HL       TCGA-C5-A7CG       TCGA-C5-A7CJ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-C5-A7UC       TCGA-DG-A2KH       TCGA-DG-A2KJ       TCGA-DG-A2KK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DG-A2KL       TCGA-DG-A2KM       TCGA-DR-A0ZL       TCGA-DS-A0VK 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A3LQ       TCGA-DS-A5RQ       TCGA-DS-A7WF       TCGA-DS-A7WH 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-DS-A7WI       TCGA-EA-A1QS       TCGA-EA-A1QT       TCGA-EA-A3HQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3HR       TCGA-EA-A3HT       TCGA-EA-A3HU       TCGA-EA-A3QD 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A3QE       TCGA-EA-A3Y4       TCGA-EA-A410       TCGA-EA-A411 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A439       TCGA-EA-A43B       TCGA-EA-A44S       TCGA-EA-A4BA 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A50E       TCGA-EA-A556       TCGA-EA-A5FO       TCGA-EA-A5O9 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A5ZD       TCGA-EA-A5ZE       TCGA-EA-A5ZF       TCGA-EA-A6QX 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EA-A78R       TCGA-EK-A2IP       TCGA-EK-A2R7       TCGA-EK-A2R8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2R9       TCGA-EK-A2RA       TCGA-EK-A2RD       TCGA-EK-A2RE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A2RJ       TCGA-EK-A2RK       TCGA-EK-A2RL       TCGA-EK-A2RN 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EK-A3GJ       TCGA-EK-A3GK       TCGA-EK-A3GN       TCGA-EX-A1H5 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A1H6       TCGA-EX-A3L1       TCGA-EX-A449       TCGA-EX-A69L 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A23K       TCGA-FU-A23L       TCGA-FU-A2QG 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3EO       TCGA-FU-A3HY       TCGA-FU-A3HZ       TCGA-FU-A3NI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A3TQ       TCGA-FU-A3TX       TCGA-FU-A3WB       TCGA-FU-A3YQ 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-FU-A40J       TCGA-FU-A57G       TCGA-FU-A5XV       TCGA-FU-A770 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HG-A2PA       TCGA-HM-A3JJ       TCGA-HM-A3JK       TCGA-HM-A4S6 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-HM-A6W2       TCGA-IR-A3L7       TCGA-IR-A3LA       TCGA-IR-A3LB 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LC       TCGA-IR-A3LF       TCGA-IR-A3LH       TCGA-IR-A3LI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-IR-A3LL       TCGA-JW-A5VG       TCGA-JW-A5VH       TCGA-JW-A5VI 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A5VJ       TCGA-JW-A5VK       TCGA-JW-A5VL       TCGA-JW-A69B 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JW-A852       TCGA-JX-A3PZ       TCGA-JX-A3Q0       TCGA-JX-A3Q8 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-JX-A5QV       TCGA-LP-A4AU       TCGA-LP-A4AV       TCGA-LP-A4AW 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-LP-A4AX       TCGA-LP-A5U2       TCGA-LP-A5U3       TCGA-LP-A7HU 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MU-A51Y       TCGA-MU-A5YI       TCGA-MY-A5BD       TCGA-MY-A5BE 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-MY-A5BF       TCGA-Q1-A5R1       TCGA-Q1-A5R2       TCGA-Q1-A5R3 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A6DT       TCGA-Q1-A6DV       TCGA-Q1-A6DW       TCGA-Q1-A73O 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-Q1-A73P       TCGA-Q1-A73Q       TCGA-Q1-A73R       TCGA-Q1-A73S 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
      TCGA-R2-A69V       TCGA-UC-A7PD       TCGA-UC-A7PF       TCGA-WL-A834 
"POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" "POU2F1 WILD-TYPE" 
D27V44, continuous
                  vv
clus               STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  POU2F1 MUTATED         0        0         0         0        0         0
  POU2F1 WILD-TYPE       4        1         1         1       28        53
                  vv
clus               STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  POU2F1 MUTATED           1        0         0          0          0         1
  POU2F1 WILD-TYPE        28        4         6          5          7        13
                  vv
clus               STAGE III STAGE IIIB STAGE IVA STAGE IVB
  POU2F1 MUTATED           0          1         0         0
  POU2F1 WILD-TYPE         1         28         2         5
D27V45, multiclass
            clus
vv           POU2F1 MUTATED POU2F1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0                1
  STAGE IA1               0                1
  STAGE IA2               0                1
  STAGE IB                0               28
  STAGE IB1               0               53
  STAGE IB2               1               28
  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               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(28) Variable = IFNGR1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  IFNGR1 MUTATED     5   1
  IFNGR1 WILD-TYPE 145  39
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               6              184 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               1               39 
$`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-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35       100.14        38.43        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-A7X3 
       15.48        20.35       147.35        17.19       155.77         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       58.88        36.76         2.66       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 
       12.36        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        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         0.92         2.17        31.36         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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       117.40        96.95        78.71 
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-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58        28.37         8.28        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       30.31         7.99        11.28         0.89        12.49         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.35        13.87        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-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        15.39        19.36        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
        3.88        11.67        93.99        26.01 

  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
            0.30             0.03 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
          173.29           210.67 
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
          34.750           19.315 
[1] "0.3 - 173.3 (34.8)" "0.0 - 210.7 (19.3)"
[1] "hr=" "2.3"
D28V2, continuous
                  vv
clus                T1  T2 T3+T4
  IFNGR1 MUTATED     0   3     0
  IFNGR1 WILD-TYPE 104  37     5
D28V3, 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"
D28V4, 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
D28V5, 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
                  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                                  21
                  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                                            3
D28V6, 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               21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                  0                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE               0                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"
D28V7, binary
                  cls
clus                 0   1
  IFNGR1 MUTATED     1   5
  IFNGR1 WILD-TYPE  31 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    5
  IFNGR1 WILD-TYPE   31  157
     clus
vv    IFNGR1 MUTATED IFNGR1 WILD-TYPE
  NO               1               31
  YES              5              157
[1] 2 2
[1] FALSE
D28V8, 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" 
D28V9, 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
D28V10, 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"
D28V11, binary
                  cls
clus                 0   1
  IFNGR1 MUTATED     1   5
  IFNGR1 WILD-TYPE  13 129
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    5
  IFNGR1 WILD-TYPE   13  129
                        clus
vv                       IFNGR1 MUTATED IFNGR1 WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO              5              129
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    3  1
  IFNGR1 WILD-TYPE 94 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      3    1
  IFNGR1 WILD-TYPE   94   30
            clus
vv           IFNGR1 MUTATED IFNGR1 WILD-TYPE
  TUMOR FREE              3               94
  WITH TUMOR              1               30
[1] 2 2
[1] FALSE
                  vv
clus               CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  IFNGR1 MUTATED        0      0       0             5       1
  IFNGR1 WILD-TYPE      5     10       6           154      13
D28V14, multiclass
               clus
vv              IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CANADA                     0                5
  RUSSIA                     0               10
  UKRAINE                    0                6
  UNITED STATES              5              154
  VIETNAM                    1               13
[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               G1 G2 G3 G4 GX
  IFNGR1 MUTATED    0  2  4  0  0
  IFNGR1 WILD-TYPE 14 86 78  1  8
D28V15, 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"
D28V16, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               27 
      TCGA-BI-A0VR       TCGA-C5-A1BJ       TCGA-C5-A1BQ       TCGA-C5-A1ME 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MF       TCGA-C5-A1MH       TCGA-C5-A3HD       TCGA-C5-A7CM 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7CO       TCGA-DG-A2KK       TCGA-DS-A3LQ       TCGA-EK-A2RA 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-EX-A69M       TCGA-FU-A2QG       TCGA-FU-A3TX       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" 
D28V17, 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" 
                  vv
clus               CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  IFNGR1 MUTATED                                             2
  IFNGR1 WILD-TYPE                                          24
                  vv
clus               CURRENT REFORMED SMOKER FOR > 15 YEARS
  IFNGR1 MUTATED                                        0
  IFNGR1 WILD-TYPE                                      8
                  vv
clus               CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  IFNGR1 MUTATED                                                 0
  IFNGR1 WILD-TYPE                                               1
                  vv
clus               CURRENT SMOKER LIFELONG NON-SMOKER
  IFNGR1 MUTATED                0                   4
  IFNGR1 WILD-TYPE             37                  89
D28V18, multiclass
                                                 clus
vv                                                IFNGR1 MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                       0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED              0
  CURRENT SMOKER                                               0
  LIFELONG NON-SMOKER                                          4
                                                 clus
vv                                                IFNGR1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                37
  LIFELONG NON-SMOKER                                           89
[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"
D28V19, continuous
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               50 
      TCGA-BI-A0VR       TCGA-C5-A1BI       TCGA-C5-A1BJ       TCGA-C5-A1BN 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1BQ       TCGA-C5-A1M7       TCGA-C5-A1ME       TCGA-C5-A1MF 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A1MI       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-A7CL       TCGA-C5-A7CO       TCGA-C5-A7UE 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-DG-A2KK       TCGA-DR-A0ZM       TCGA-DS-A5RQ       TCGA-EA-A556 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-EK-A2RA       TCGA-EX-A1H5       TCGA-FU-A2QG       TCGA-FU-A3EO 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-FU-A3TQ       TCGA-FU-A3TX       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" 
D28V20, continuous
                  vv
clus               COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  IFNGR1 MUTATED             1        1             0        0        1
  IFNGR1 WILD-TYPE          19       53            12        1        6
D28V21, multiclass
               clus
vv              IFNGR1 MUTATED IFNGR1 WILD-TYPE
  COMBINATION                1               19
  EXTERNAL                   1               53
  EXTERNAL BEAM              0               12
  IMPLANTS                   0                1
  INTERNAL                   1                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"
D28V22, 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
                  vv
clus               DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  IFNGR1 MUTATED                    0                0                   1
  IFNGR1 WILD-TYPE                  2                2                  19
                  vv
clus               REGIONAL SITE
  IFNGR1 MUTATED               1
  IFNGR1 WILD-TYPE             3
D28V23, multiclass
[1] "Remove cluster labels:" "IFNGR1 MUTATED"        
clus
  IFNGR1 MUTATED IFNGR1 WILD-TYPE 
               2               26 
      TCGA-C5-A0TN       TCGA-C5-A1BF       TCGA-C5-A1BQ       TCGA-C5-A2LZ 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7CK       TCGA-C5-A7CL       TCGA-C5-A7CM       TCGA-C5-A7CO 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-C5-A7UE       TCGA-C5-A7X3       TCGA-DG-A2KL       TCGA-DS-A7WF 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-EA-A43B       TCGA-EA-A5FO       TCGA-EX-A3L1       TCGA-FU-A23L 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-FU-A3HY       TCGA-HM-A3JJ       TCGA-HM-A4S6       TCGA-IR-A3LF 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-IR-A3LH       TCGA-JW-A5VG       TCGA-JX-A3Q0       TCGA-JX-A5QV 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
      TCGA-R2-A69V       TCGA-WL-A834 
"IFNGR1 WILD-TYPE" "IFNGR1 WILD-TYPE" 
D28V24, binary
                  cls
clus                0  1
  IFNGR1 MUTATED    1  0
  IFNGR1 WILD-TYPE 15  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR1 MUTATED      1    0
  IFNGR1 WILD-TYPE   15    4
     clus
vv    IFNGR1 MUTATED IFNGR1 WILD-TYPE
  CGY              1               15
  GY               0                4
[1] 2 2
[1] FALSE
D28V25, continuous
D28V26, continuous
D28V27, continuous
D28V28, continuous
D28V29, continuous
D28V30, continuous
                  vv
clus               MACROSCOPIC PARAMETRIAL INVOLVEMENT
  IFNGR1 MUTATED                                     0
  IFNGR1 WILD-TYPE                                   2
                  vv
clus               MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  IFNGR1 MUTATED                                     0                       0
  IFNGR1 WILD-TYPE                                   7                      28
                  vv
clus               POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  IFNGR1 MUTATED                         0                       0
  IFNGR1 WILD-TYPE                       1                       6
D28V31, multiclass
                  vv
clus               INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  IFNGR1 MUTATED                                               0
  IFNGR1 WILD-TYPE                                             2
                  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
D28V32, 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)                                                               2
  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"
D28V33, 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
D28V34, continuous
D28V35, continuous
D28V36, 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
D28V37, continuous
                  vv
clus               CURRENT USER FORMER USER NEVER USED
  IFNGR1 MUTATED              0           2          3
  IFNGR1 WILD-TYPE            8          41         43
D28V38, 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"
D28V39, continuous
D28V40, 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         0     0
  IFNGR1 WILD-TYPE           2        16     1
D28V41, multiclass
D28V42, continuous
                  vv
clus               T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  IFNGR1 MUTATED      0   0    0    0  0   1    0    1   1  0   0  0  0
  IFNGR1 WILD-TYPE    1  21   60   22  4   6    6    9  12  1   2  2  9
D28V43, multiclass
      clus
vv     IFNGR1 MUTATED IFNGR1 WILD-TYPE
  T1A1              0                1
  T1B               0               21
  T1B1              0               60
  T1B2              0               22
  T2                0                4
  T2A               1                6
  T2A1              0                6
  T2A2              1                9
  T2B               1               12
  T3                0                1
  T3B               0                2
  T4                0                2
  TX                0                9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V44, 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
D28V45, 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"

Clustering(29) Variable = IGFN1 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  IGFN1 MUTATED     7   3
  IGFN1 WILD-TYPE 143  37
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             10             180 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              3              37 
$`IGFN1 MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1MK TCGA-DS-A3LQ TCGA-EA-A3QD TCGA-EA-A5FO TCGA-EK-A2PG 
       19.86         2.43        22.98        13.05        26.79         1.51 
TCGA-EK-A3GK TCGA-JW-A5VL TCGA-JX-A3Q8 TCGA-UC-A7PF 
        0.10        15.58        30.31        93.99 

$`IGFN1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46        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        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       28.90        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-A3QE 
       12.36        37.35        30.90        31.36        33.30        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50        26.40        24.56        14.50        26.01        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         7.46        14.89        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64        19.27         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         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 
      117.40        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-A69B 
       27.42         3.29        24.56        21.44        20.48        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        8.28        21.11       195.85         7.99        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        13.87        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-WL-A834 
       15.39        19.36        19.59         3.88        11.67        26.01 

  IGFN1 MUTATED IGFN1 WILD-TYPE 
           0.10            0.03 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
          93.99          210.67 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
          17.72           19.69 
[1] "0.1 - 94.0 (17.7)"  "0.0 - 210.7 (19.7)"
[1] "hr=" "2.1"
D29V2, continuous
                 vv
clus              T1 T2 T3+T4
  IGFN1 MUTATED    7  0     1
  IGFN1 WILD-TYPE 97 40     4
D29V3, multiclass
       clus
vv      IGFN1 MUTATED IGFN1 WILD-TYPE
  T1                7              97
  T2                0              40
  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"
D29V4, binary
                 cls
clus               0  1
  IGFN1 MUTATED    4  3
  IGFN1 WILD-TYPE 91 41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      4    3
  IGFN1 WILD-TYPE   91   41
   clus
vv  IGFN1 MUTATED IGFN1 WILD-TYPE
  0             4              91
  1             3              41
[1] 2 2
[1] FALSE
D29V5, binary
                 cls
clus               0  1
  IGFN1 MUTATED    5  0
  IGFN1 WILD-TYPE 74  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      5    0
  IGFN1 WILD-TYPE   74    4
   clus
vv  IGFN1 MUTATED IGFN1 WILD-TYPE
  0             5              74
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  IGFN1 MUTATED               0                                9
  IGFN1 WILD-TYPE             4                              149
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  IGFN1 MUTATED                                               0
  IGFN1 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  IGFN1 MUTATED                                     2
  IGFN1 WILD-TYPE                                  20
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  IGFN1 MUTATED                                           0
  IGFN1 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  IGFN1 MUTATED                                              0
  IGFN1 WILD-TYPE                                            3
D29V6, multiclass
                                               clus
vv                                              IGFN1 MUTATED IGFN1 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          9             149
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       2              20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D29V7, binary
                 cls
clus                0   1
  IGFN1 MUTATED     2   9
  IGFN1 WILD-TYPE  30 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      2    9
  IGFN1 WILD-TYPE   30  153
     clus
vv    IGFN1 MUTATED IGFN1 WILD-TYPE
  NO              2              30
  YES             9             153
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
D29V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFN1 MUTATED                                  1     2
  IGFN1 WILD-TYPE                                7    17
                 vv
clus              BLACK OR AFRICAN AMERICAN
  IGFN1 MUTATED                           1
  IGFN1 WILD-TYPE                        15
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGFN1 MUTATED                                           0     5
  IGFN1 WILD-TYPE                                         1   133
D29V10, multiclass
                                           clus
vv                                          IGFN1 MUTATED IGFN1 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                                                 5             133
[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"
D29V11, binary
                 cls
clus                0   1
  IGFN1 MUTATED     1   7
  IGFN1 WILD-TYPE  13 127
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      1    7
  IGFN1 WILD-TYPE   13  127
                        clus
vv                       IGFN1 MUTATED IGFN1 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             7             127
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                 cls
clus               0  1
  IGFN1 MUTATED    5  1
  IGFN1 WILD-TYPE 92 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      5    1
  IGFN1 WILD-TYPE   92   30
            clus
vv           IGFN1 MUTATED IGFN1 WILD-TYPE
  TUMOR FREE             5              92
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  IGFN1 MUTATED        0      0       1             9       1
  IGFN1 WILD-TYPE      5     10       5           150      13
D29V14, multiclass
               clus
vv              IGFN1 MUTATED IGFN1 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   1               5
  UNITED STATES             9             150
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  IGFN1 MUTATED    1  4  6  0  0
  IGFN1 WILD-TYPE 13 84 76  1  8
D29V15, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  G1             1              13
  G2             4              84
  G3             6              76
  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"
D29V16, continuous
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              2              27 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1ME 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2      TCGA-C5-A3HD 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-EK-A2RA 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX      TCGA-FU-A3WB 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7      TCGA-IR-A3LB 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
D29V17, continuous
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  IGFN1 MUTATED                                             1
  IGFN1 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  IGFN1 MUTATED                                        1
  IGFN1 WILD-TYPE                                      7
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  IGFN1 MUTATED                                                 0
  IGFN1 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  IGFN1 MUTATED                1                   6
  IGFN1 WILD-TYPE             36                  87
D29V18, multiclass
                                                 clus
vv                                                IGFN1 MUTATED IGFN1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      1               7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         6              87
[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"
D29V19, continuous
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              1              51 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1M7      TCGA-C5-A1ME      TCGA-C5-A1MF 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CL      TCGA-C5-A7CO 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DR-A0ZM      TCGA-DS-A5RQ 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5      TCGA-FU-A2QG 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ      TCGA-FU-A3TX 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV      TCGA-FU-A770 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LB 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK      TCGA-JX-A3Q0 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
D29V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  IGFN1 MUTATED             1        2             1        0        1
  IGFN1 WILD-TYPE          19       52            11        1        6
D29V21, multiclass
               clus
vv              IGFN1 MUTATED IGFN1 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  2              52
  EXTERNAL BEAM             1              11
  IMPLANTS                  0               1
  INTERNAL                  1               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"
D29V22, binary
                 cls
clus               0  1
  IGFN1 MUTATED    1  1
  IGFN1 WILD-TYPE 25  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      1    1
  IGFN1 WILD-TYPE   25    2
                         clus
vv                        IGFN1 MUTATED IGFN1 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             1               2
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  IGFN1 MUTATED                    0                0                   1
  IGFN1 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  IGFN1 MUTATED               1
  IGFN1 WILD-TYPE             3
D29V23, multiclass
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              2              26 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A2LZ      TCGA-C5-A7CK 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DS-A7WF 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EX-A3L1      TCGA-FU-A23L      TCGA-FU-A3HY 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6      TCGA-IR-A3LF 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0      TCGA-JX-A5QV 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-R2-A69V      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
D29V24, binary
                 cls
clus               0  1
  IGFN1 MUTATED    0  1
  IGFN1 WILD-TYPE 16  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      0    1
  IGFN1 WILD-TYPE   16    3
     clus
vv    IGFN1 MUTATED IGFN1 WILD-TYPE
  CGY             0              16
  GY              1               3
[1] 2 2
[1] FALSE
D29V25, continuous
D29V26, continuous
D29V27, continuous
D29V28, continuous
D29V29, continuous
D29V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  IGFN1 MUTATED                                     0
  IGFN1 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  IGFN1 MUTATED                                     0                       1
  IGFN1 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  IGFN1 MUTATED                         0                       0
  IGFN1 WILD-TYPE                       1                       6
D29V31, multiclass
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              1              43 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-EA-A50E 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-UC-A7PD      TCGA-WL-A834 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  IGFN1 MUTATED                                               0
  IGFN1 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  IGFN1 MUTATED                                                0
  IGFN1 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  IGFN1 MUTATED                                                                                   5
  IGFN1 WILD-TYPE                                                                                55
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  IGFN1 MUTATED                                                                                              4
  IGFN1 WILD-TYPE                                                                                           84
D29V32, multiclass
                                                                                              clus
vv                                                                                             IGFN1 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)             4
                                                                                              clus
vv                                                                                             IGFN1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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)              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"
D29V33, binary
                 cls
clus               0  1
  IGFN1 MUTATED    2  4
  IGFN1 WILD-TYPE 61 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      2    4
  IGFN1 WILD-TYPE   61   63
         clus
vv        IGFN1 MUTATED IGFN1 WILD-TYPE
  ABSENT              2              61
  PRESENT             4              63
[1] 2 2
[1] FALSE
D29V34, continuous
D29V35, continuous
D29V36, binary
                 cls
clus               0  1
  IGFN1 MUTATED    2  4
  IGFN1 WILD-TYPE 37 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      2    4
  IGFN1 WILD-TYPE   37   82
                                          clus
vv                                         IGFN1 MUTATED IGFN1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 2              37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             4              82
[1] 2 2
[1] FALSE
D29V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  IGFN1 MUTATED              1           3          0
  IGFN1 WILD-TYPE            7          40         46
D29V38, multiclass
              clus
vv             IGFN1 MUTATED IGFN1 WILD-TYPE
  CURRENT USER             1               7
  FORMER USER              3              40
  NEVER USED               0              46
[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"
D29V39, continuous
D29V40, binary
                 cls
clus               0  1
  IGFN1 MUTATED    3  1
  IGFN1 WILD-TYPE 85 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      3    1
  IGFN1 WILD-TYPE   85   15
         clus
vv        IGFN1 MUTATED IGFN1 WILD-TYPE
  ABSENT              3              85
  PRESENT             1              15
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  IGFN1 MUTATED             1         1     0
  IGFN1 WILD-TYPE           1        15     1
D29V41, multiclass
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              2              17 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-EK-A2H0      TCGA-EK-A2H1 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-HM-A3JJ 
"IGFN1 WILD-TYPE" 
D29V42, continuous
[1] "Remove cluster labels:" "IGFN1 MUTATED"         
clus
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              1               9 
     TCGA-C5-A1BN      TCGA-C5-A1MH      TCGA-C5-A1ML      TCGA-C5-A1MN 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-EK-A2RO      TCGA-HM-A3JK      TCGA-JW-A852 
"IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" "IGFN1 WILD-TYPE" 
     TCGA-MU-A51Y 
"IGFN1 WILD-TYPE" 
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  IGFN1 MUTATED      0   1    5    1  0   0    0    0   0  0   1  0  0
  IGFN1 WILD-TYPE    1  20   55   21  4   7    6   10  13  1   1  2  9
D29V43, multiclass
      clus
vv     IGFN1 MUTATED IGFN1 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             5              55
  T1B2             1              21
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              0              13
  T3               0               1
  T3B              1               1
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  IGFN1 MUTATED         0        0         0         0        1         4
  IGFN1 WILD-TYPE       4        1         1         1       27        49
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  IGFN1 MUTATED           1        0         0          0          0         0
  IGFN1 WILD-TYPE        28        4         6          5          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  IGFN1 MUTATED           0          4         0         0
  IGFN1 WILD-TYPE         1         25         2         5
D29V45, multiclass
            clus
vv           IGFN1 MUTATED IGFN1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              4              49
  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             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(30) Variable = RPGR MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  RPGR MUTATED     6   3
  RPGR WILD-TYPE 144  37
  RPGR MUTATED RPGR WILD-TYPE 
             9            181 
  RPGR MUTATED RPGR WILD-TYPE 
             3             37 
$`RPGR MUTATED`
TCGA-C5-A1BQ TCGA-DS-A0VL TCGA-EK-A3GK TCGA-HG-A2PA TCGA-IR-A3LA TCGA-IR-A3LH 
       19.86         2.66         0.10        25.41       137.16        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-Q1-A5R2 
       81.96        29.85        16.41 

$`RPGR WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        87.75        58.88        36.76       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.97         1.12        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LL TCGA-JW-A5VG 
      147.39        66.81       117.40        96.95        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       195.85        30.31         7.99        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        13.87 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       34.62        54.81        35.05        20.84        15.58        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  RPGR MUTATED RPGR WILD-TYPE 
          0.10           0.03 
  RPGR MUTATED RPGR WILD-TYPE 
        137.16         210.67 
  RPGR MUTATED RPGR WILD-TYPE 
         25.41          19.36 
[1] "0.1 - 137.2 (25.4)" "0.0 - 210.7 (19.4)"
[1] "hr=" "1.3"
D30V2, continuous
                vv
clus             T1 T2 T3+T4
  RPGR MUTATED    5  2     0
  RPGR WILD-TYPE 99 38     5
D30V3, multiclass
       clus
vv      RPGR MUTATED RPGR WILD-TYPE
  T1               5             99
  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"
D30V4, binary
                cls
clus              0  1
  RPGR MUTATED    6  1
  RPGR WILD-TYPE 89 43
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      6    1
  RPGR WILD-TYPE   89   43
   clus
vv  RPGR MUTATED RPGR WILD-TYPE
  0            6             89
  1            1             43
[1] 2 2
[1] FALSE
D30V5, binary
                cls
clus              0  1
  RPGR MUTATED    5  1
  RPGR WILD-TYPE 74  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      5    1
  RPGR WILD-TYPE   74    3
   clus
vv  RPGR MUTATED RPGR WILD-TYPE
  0            5             74
  1            1              3
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  RPGR MUTATED               0                                6
  RPGR WILD-TYPE             4                              152
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  RPGR MUTATED                                               0
  RPGR WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  RPGR MUTATED                                     2
  RPGR WILD-TYPE                                  20
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  RPGR MUTATED                                           1
  RPGR WILD-TYPE                                         1
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  RPGR MUTATED                                              0
  RPGR WILD-TYPE                                            3
D30V6, multiclass
                                               clus
vv                                              RPGR MUTATED RPGR WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         6            152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      2             20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                1              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D30V7, binary
                cls
clus               0   1
  RPGR MUTATED     0   9
  RPGR WILD-TYPE  32 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      0    9
  RPGR WILD-TYPE   32  153
     clus
vv    RPGR MUTATED RPGR WILD-TYPE
  NO             0             32
  YES            9            153
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "RPGR MUTATED"          
clus
  RPGR MUTATED RPGR WILD-TYPE 
             2             55 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
D30V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPGR MUTATED                                  0     0
  RPGR WILD-TYPE                                8    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  RPGR MUTATED                           1
  RPGR WILD-TYPE                        15
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPGR MUTATED                                           0     8
  RPGR WILD-TYPE                                         1   130
D30V10, multiclass
                                           clus
vv                                          RPGR MUTATED RPGR 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                                                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"
D30V11, binary
                cls
clus               0   1
  RPGR MUTATED     0   4
  RPGR WILD-TYPE  14 130
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      0    4
  RPGR WILD-TYPE   14  130
                        clus
vv                       RPGR MUTATED RPGR WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            4            130
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                cls
clus              0  1
  RPGR MUTATED    5  2
  RPGR WILD-TYPE 92 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      5    2
  RPGR WILD-TYPE   92   29
            clus
vv           RPGR MUTATED RPGR WILD-TYPE
  TUMOR FREE            5             92
  WITH TUMOR            2             29
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  RPGR MUTATED        0      0       0             9       0
  RPGR WILD-TYPE      5     10       6           150      14
D30V14, multiclass
               clus
vv              RPGR MUTATED RPGR WILD-TYPE
  CANADA                   0              5
  RUSSIA                   0             10
  UKRAINE                  0              6
  UNITED STATES            9            150
  VIETNAM                  0             14
[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             G1 G2 G3 G4 GX
  RPGR MUTATED    0  4  4  1  0
  RPGR WILD-TYPE 14 84 78  0  8
D30V15, multiclass
    clus
vv   RPGR MUTATED RPGR WILD-TYPE
  G1            0             14
  G2            4             84
  G3            4             78
  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"
D30V16, continuous
[1] "Remove cluster labels:" "RPGR MUTATED"          
clus
  RPGR MUTATED RPGR WILD-TYPE 
             2             27 
    TCGA-BI-A0VR     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1ME 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DS-A3LQ 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3TX 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
D30V17, continuous
[1] "Remove cluster labels:" "RPGR MUTATED"          
clus
  RPGR MUTATED RPGR WILD-TYPE 
             2             55 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  RPGR MUTATED                                             2
  RPGR WILD-TYPE                                          24
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  RPGR MUTATED                                        0
  RPGR WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  RPGR MUTATED                                                 0              1
  RPGR WILD-TYPE                                               1             36
                vv
clus             LIFELONG NON-SMOKER
  RPGR MUTATED                     5
  RPGR WILD-TYPE                  88
D30V18, multiclass
                                                 clus
vv                                                RPGR MUTATED RPGR WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                2             24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             1             36
  LIFELONG NON-SMOKER                                        5             88
[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"
D30V19, continuous
[1] "Remove cluster labels:" "RPGR MUTATED"          
clus
  RPGR MUTATED RPGR WILD-TYPE 
             2             50 
    TCGA-BI-A0VR     TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BL 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME     TCGA-C5-A1MF 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CL     TCGA-C5-A7CO 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DR-A0ZM     TCGA-DS-A5RQ 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-EA-A556     TCGA-EK-A2RA     TCGA-EX-A1H5     TCGA-FU-A2QG 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ     TCGA-FU-A3TX 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0     TCGA-MU-A5YI 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S     TCGA-RA-A741 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" 
D30V20, continuous
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  RPGR MUTATED             0        6             0        0        0
  RPGR WILD-TYPE          20       48            12        1        7
D30V21, multiclass
               clus
vv              RPGR MUTATED RPGR WILD-TYPE
  COMBINATION              0             20
  EXTERNAL                 6             48
  EXTERNAL BEAM            0             12
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D30V22, binary
                cls
clus              0  1
  RPGR MUTATED    0  0
  RPGR WILD-TYPE 26  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      0    0
  RPGR WILD-TYPE   26    3
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  RPGR MUTATED                    0                0                   2
  RPGR WILD-TYPE                  2                2                  18
                vv
clus             REGIONAL SITE
  RPGR MUTATED               0
  RPGR WILD-TYPE             4
D30V23, multiclass
[1] "Remove cluster labels:" "RPGR MUTATED"          
clus
  RPGR MUTATED RPGR WILD-TYPE 
             2             26 
    TCGA-C5-A0TN     TCGA-C5-A1BF     TCGA-C5-A2LZ     TCGA-C5-A7CK 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UE 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DS-A7WF 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A5FO     TCGA-EX-A3L1     TCGA-FU-A23L 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A4S6 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-JW-A5VG     TCGA-JX-A3Q0     TCGA-JX-A5QV 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" "RPGR WILD-TYPE" 
    TCGA-R2-A69V     TCGA-WL-A834 
"RPGR WILD-TYPE" "RPGR WILD-TYPE" 
D30V24, binary
                cls
clus              0  1
  RPGR MUTATED    1  0
  RPGR WILD-TYPE 15  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      1    0
  RPGR WILD-TYPE   15    4
     clus
vv    RPGR MUTATED RPGR WILD-TYPE
  CGY            1             15
  GY             0              4
[1] 2 2
[1] FALSE
D30V25, continuous
D30V26, continuous
D30V27, continuous
D30V28, continuous
D30V29, continuous
D30V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  RPGR MUTATED                                     0
  RPGR WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  RPGR MUTATED                                     2                       1
  RPGR WILD-TYPE                                   5                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  RPGR MUTATED                         0                       1
  RPGR WILD-TYPE                       1                       5
D30V31, multiclass
                                     clus
vv                                    RPGR MUTATED RPGR WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT            0              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT            2              5
  OTHER LOCATION, SPECIFY                        1             27
  POSITIVE BLADDER MARGIN                        0              1
  POSITIVE VAGINAL MARGIN                        1              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)
  RPGR MUTATED                                               0
  RPGR WILD-TYPE                                             2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  RPGR MUTATED                                                1
  RPGR WILD-TYPE                                              9
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  RPGR MUTATED                                                                                   4
  RPGR WILD-TYPE                                                                                56
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  RPGR MUTATED                                                                                              3
  RPGR WILD-TYPE                                                                                           85
D30V32, multiclass
                                                                                              clus
vv                                                                                             RPGR 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)            3
                                                                                              clus
vv                                                                                             RPGR WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             2
  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)             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"
D30V33, binary
                cls
clus              0  1
  RPGR MUTATED    1  5
  RPGR WILD-TYPE 62 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      1    5
  RPGR WILD-TYPE   62   62
         clus
vv        RPGR MUTATED RPGR WILD-TYPE
  ABSENT             1             62
  PRESENT            5             62
[1] 2 2
[1] FALSE
D30V34, continuous
D30V35, continuous
D30V36, binary
                cls
clus              0  1
  RPGR MUTATED    1  3
  RPGR WILD-TYPE 38 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      1    3
  RPGR WILD-TYPE   38   83
                                          clus
vv                                         RPGR MUTATED RPGR WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                1             38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            3             83
[1] 2 2
[1] FALSE
D30V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  RPGR MUTATED              1           2          4
  RPGR WILD-TYPE            7          41         42
D30V38, multiclass
              clus
vv             RPGR MUTATED RPGR WILD-TYPE
  CURRENT USER            1              7
  FORMER USER             2             41
  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"
D30V39, continuous
D30V40, binary
                cls
clus              0  1
  RPGR MUTATED    6  1
  RPGR WILD-TYPE 82 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      6    1
  RPGR WILD-TYPE   82   15
         clus
vv        RPGR MUTATED RPGR WILD-TYPE
  ABSENT             6             82
  PRESENT            1             15
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  RPGR MUTATED             0         0     0
  RPGR WILD-TYPE           2        16     1
D30V41, multiclass
D30V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  RPGR MUTATED      0   0    3    2  0   0    1    0   1  0   0  0  1
  RPGR WILD-TYPE    1  21   57   20  4   7    5   10  12  1   2  2  8
D30V43, multiclass
      clus
vv     RPGR MUTATED RPGR WILD-TYPE
  T1A1            0              1
  T1B             0             21
  T1B1            3             57
  T1B2            2             20
  T2              0              4
  T2A             0              7
  T2A1            1              5
  T2A2            0             10
  T2B             1             12
  T3              0              1
  T3B             0              2
  T4              0              2
  TX              1              8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  RPGR MUTATED         0        0         0         0        1         2
  RPGR WILD-TYPE       4        1         1         1       27        51
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  RPGR MUTATED           2        0         0          1          0         0
  RPGR WILD-TYPE        27        4         6          4          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  RPGR MUTATED           0          1         0         1
  RPGR WILD-TYPE         1         28         2         4
D30V45, multiclass
            clus
vv           RPGR MUTATED RPGR WILD-TYPE
  STAGE I               0              4
  STAGE IA              0              1
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              1             27
  STAGE IB1             2             51
  STAGE IB2             2             27
  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            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(31) Variable = CASP8 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     7   2
  CASP8 WILD-TYPE 143  38
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             181 
  CASP8 MUTATED CASP8 WILD-TYPE 
              2              38 
$`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         2.66         8.28        19.79 
TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-MY-A5BD 
       36.36       195.85        54.81 

$`CASP8 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       83.05        78.35       100.14        38.43        33.24        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-A7UH TCGA-C5-A7X3 
       15.48        20.35       147.35        17.19       131.11         9.34 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ 
       58.88        36.76       117.99       118.65        28.90        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18        17.52        39.55        12.36        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        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        14.50        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        47.77         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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       117.40        96.95        78.71        81.96        29.85 
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        30.31         7.99        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        13.87 
TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       34.62        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  CASP8 MUTATED CASP8 WILD-TYPE 
           2.66            0.03 
  CASP8 MUTATED CASP8 WILD-TYPE 
         195.85          210.67 
  CASP8 MUTATED CASP8 WILD-TYPE 
          36.36           19.27 
[1] "2.7 - 195.8 (36.4)" "0.0 - 210.7 (19.3)"
[1] "hr=" "1.5"
D31V2, continuous
                 vv
clus               T1  T2 T3+T4
  CASP8 MUTATED     3   2     1
  CASP8 WILD-TYPE 101  38     4
D31V3, 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"
D31V4, 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
D31V5, 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
                 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                                  22
                 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                                            3
D31V6, 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              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D31V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     1   8
  CASP8 WILD-TYPE  31 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      1    8
  CASP8 WILD-TYPE   31  154
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              1              31
  YES             8             154
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, 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
D31V10, 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"
D31V11, binary
                 cls
clus                0   1
  CASP8 MUTATED     1   5
  CASP8 WILD-TYPE  13 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      1    5
  CASP8 WILD-TYPE   13  129
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             5             129
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                 cls
clus               0  1
  CASP8 MUTATED    7  1
  CASP8 WILD-TYPE 90 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      7    1
  CASP8 WILD-TYPE   90   30
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  TUMOR FREE             7              90
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  CASP8 MUTATED        0      0       0             9       0
  CASP8 WILD-TYPE      5     10       6           150      14
D31V14, multiclass
               clus
vv              CASP8 MUTATED CASP8 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             9             150
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  CASP8 MUTATED    1  7  1  0  0
  CASP8 WILD-TYPE 13 81 81  1  8
D31V15, 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"
D31V16, continuous
D31V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  CASP8 MUTATED                                             3
  CASP8 WILD-TYPE                                          23
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  CASP8 MUTATED                                        0
  CASP8 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  CASP8 MUTATED                                                 0
  CASP8 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  CASP8 MUTATED                1                   5
  CASP8 WILD-TYPE             36                  88
D31V18, multiclass
                                                 clus
vv                                                CASP8 MUTATED CASP8 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 3              23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         5              88
[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"
D31V19, continuous
D31V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  CASP8 MUTATED             1        6             0        0        0
  CASP8 WILD-TYPE          19       48            12        1        7
D31V21, multiclass
               clus
vv              CASP8 MUTATED CASP8 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  6              48
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D31V22, 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
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  CASP8 MUTATED                    0                0                   3
  CASP8 WILD-TYPE                  2                2                  17
                 vv
clus              REGIONAL SITE
  CASP8 MUTATED               0
  CASP8 WILD-TYPE             4
D31V23, multiclass
                     clus
vv                    CASP8 MUTATED CASP8 WILD-TYPE
  DISTANT RECURRENCE              0               2
  LOCAL RECURRENCE                0               2
  PRIMARY TUMOR FIELD             3              17
  REGIONAL SITE                   0               4
[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"
D31V24, binary
                 cls
clus               0  1
  CASP8 MUTATED    1  0
  CASP8 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      1    0
  CASP8 WILD-TYPE   15    4
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D31V25, continuous
D31V26, continuous
D31V27, continuous
D31V28, continuous
D31V29, continuous
D31V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  CASP8 MUTATED                                     0
  CASP8 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  CASP8 MUTATED                                     0                       1
  CASP8 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  CASP8 MUTATED                         0                       0
  CASP8 WILD-TYPE                       1                       6
D31V31, multiclass
[1] "Remove cluster labels:" "CASP8 MUTATED"         
clus
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              43 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VM 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-UC-A7PD      TCGA-WL-A834 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  CASP8 MUTATED                                               0
  CASP8 WILD-TYPE                                             2
                 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
D31V32, 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)                                                              2
  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"
D31V33, 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
D31V34, continuous
D31V35, continuous
D31V36, 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
D31V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  CASP8 MUTATED              0           1          4
  CASP8 WILD-TYPE            8          42         42
D31V38, 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"
D31V39, continuous
D31V40, 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         1     0
  CASP8 WILD-TYPE           2        15     1
D31V41, multiclass
[1] "Remove cluster labels:" "CASP8 MUTATED"         
clus
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
D31V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  CASP8 MUTATED      0   0    3    0  0   0    0    1   1  1   0  0  0
  CASP8 WILD-TYPE    1  21   57   22  4   7    6    9  12  0   2  2  9
D31V43, multiclass
      clus
vv     CASP8 MUTATED CASP8 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             3              57
  T1B2             0              22
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             1               9
  T2B              1              12
  T3               1               0
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V44, 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
D31V45, 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(32) Variable = GAS6 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  GAS6 MUTATED     3   1
  GAS6 WILD-TYPE 147  39
  GAS6 MUTATED GAS6 WILD-TYPE 
             4            186 
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             39 
$`GAS6 MUTATED`
TCGA-C5-A1BQ TCGA-EA-A5O9 TCGA-LP-A4AW TCGA-Q1-A73O 
       19.86        13.91         0.89        14.07 

$`GAS6 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         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       117.40 
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       195.85        30.31         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
       12.49         0.30         0.82        13.35        13.87        34.62 
TCGA-MY-A5BD TCGA-MY-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-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        9.04        16.14        17.56        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  GAS6 MUTATED GAS6 WILD-TYPE 
          0.89           0.03 
  GAS6 MUTATED GAS6 WILD-TYPE 
         19.86         210.67 
  GAS6 MUTATED GAS6 WILD-TYPE 
         13.99          20.07 
[1] "0.9 - 19.9 (14.0)"  "0.0 - 210.7 (20.1)"
[1] "hr=" "3.4"
D32V2, continuous
                vv
clus              T1  T2 T3+T4
  GAS6 MUTATED     2   0     0
  GAS6 WILD-TYPE 102  40     5
D32V3, multiclass
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2            147 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BK     TCGA-C5-A1BM     TCGA-C5-A1M5 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MP 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A3HE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A439     TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5ZD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2IP     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RN     TCGA-EK-A3GJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M     TCGA-FU-A23K 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ     TCGA-FU-A3TX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J     TCGA-FU-A57G 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA     TCGA-HM-A3JJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AX     TCGA-LP-A5U2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A5U3     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A6DV     TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V4, binary
                cls
clus              0  1
  GAS6 MUTATED    2  0
  GAS6 WILD-TYPE 93 44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      2    0
  GAS6 WILD-TYPE   93   44
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0            2             93
  1            0             44
[1] 2 2
[1] FALSE
D32V5, binary
                cls
clus              0  1
  GAS6 MUTATED    2  0
  GAS6 WILD-TYPE 77  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      2    0
  GAS6 WILD-TYPE   77    4
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0            2             77
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  GAS6 MUTATED               0                                4
  GAS6 WILD-TYPE             4                              154
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  GAS6 MUTATED                                               0
  GAS6 WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  GAS6 MUTATED                                     0
  GAS6 WILD-TYPE                                  22
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  GAS6 MUTATED                                           0
  GAS6 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  GAS6 MUTATED                                              0
  GAS6 WILD-TYPE                                            3
D32V6, multiclass
                                               clus
vv                                              GAS6 MUTATED GAS6 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         4            154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D32V7, binary
                cls
clus               0   1
  GAS6 MUTATED     0   4
  GAS6 WILD-TYPE  32 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0    4
  GAS6 WILD-TYPE   32  158
     clus
vv    GAS6 MUTATED GAS6 WILD-TYPE
  NO             0             32
  YES            4            158
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V9, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1            120 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2M1     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-C5-A7UE     TCGA-DG-A2KH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3Y4 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B     TCGA-EA-A44S 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A6QX     TCGA-EK-A2RA     TCGA-EK-A2RO     TCGA-EK-A3GK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A40J     TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JX-A3PZ     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A7HU     TCGA-MU-A51Y 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A6DV     TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAS6 MUTATED                                  0     1
  GAS6 WILD-TYPE                                8    18
                vv
clus             BLACK OR AFRICAN AMERICAN
  GAS6 MUTATED                           0
  GAS6 WILD-TYPE                        16
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GAS6 MUTATED                                           0     2
  GAS6 WILD-TYPE                                         1   136
D32V10, multiclass
                                           clus
vv                                          GAS6 MUTATED GAS6 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                                                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"
D32V11, binary
                cls
clus               0   1
  GAS6 MUTATED     1   3
  GAS6 WILD-TYPE  13 131
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      1    3
  GAS6 WILD-TYPE   13  131
                        clus
vv                       GAS6 MUTATED GAS6 WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            3            131
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                cls
clus              0  1
  GAS6 MUTATED    3  0
  GAS6 WILD-TYPE 94 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      3    0
  GAS6 WILD-TYPE   94   31
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  TUMOR FREE            3             94
  WITH TUMOR            0             31
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  GAS6 MUTATED        0      0       1             2       1
  GAS6 WILD-TYPE      5     10       5           157      13
D32V14, multiclass
               clus
vv              GAS6 MUTATED GAS6 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   0             10
  UKRAINE                  1              5
  UNITED STATES            2            157
  VIETNAM                  1             13
[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             G1 G2 G3 G4 GX
  GAS6 MUTATED    1  2  0  0  1
  GAS6 WILD-TYPE 13 86 82  1  7
D32V15, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  G1            1             13
  G2            2             86
  G3            0             82
  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"
D32V16, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             28 
    TCGA-BI-A0VR     TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A2M2     TCGA-C5-A3HD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DS-A3LQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3TX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JX-A3Q0     TCGA-MU-A5YI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73S     TCGA-RA-A741     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V17, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1ML 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK     TCGA-C5-A7CL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DG-A2KL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  GAS6 MUTATED                                             1
  GAS6 WILD-TYPE                                          25
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  GAS6 MUTATED                                        0
  GAS6 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  GAS6 MUTATED                                                 0              0
  GAS6 WILD-TYPE                                               1             37
                vv
clus             LIFELONG NON-SMOKER
  GAS6 MUTATED                     3
  GAS6 WILD-TYPE                  90
D32V18, multiclass
                                                 clus
vv                                                GAS6 MUTATED GAS6 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                1             25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             0             37
  LIFELONG NON-SMOKER                                        3             90
[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"
D32V19, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             51 
    TCGA-BI-A0VR     TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1M7     TCGA-C5-A1ME     TCGA-C5-A1MF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2     TCGA-C5-A3HD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CL     TCGA-C5-A7CO 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7UE     TCGA-DG-A2KK     TCGA-DR-A0ZM     TCGA-DS-A5RQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EK-A2RA     TCGA-EX-A1H5     TCGA-FU-A2QG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ     TCGA-FU-A3TX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V20, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2             80 
    TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1M6     TCGA-C5-A1M8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MQ     TCGA-C5-A2LT     TCGA-C5-A2LX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A3HD     TCGA-C5-A3HF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7UE     TCGA-C5-A7UH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A3QD     TCGA-EA-A3Y4     TCGA-EA-A43B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A5FO     TCGA-EK-A2H0 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-FU-A23L     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VI     TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  GAS6 MUTATED             0        3             0        0        0
  GAS6 WILD-TYPE          20       51            12        1        7
D32V21, multiclass
               clus
vv              GAS6 MUTATED GAS6 WILD-TYPE
  COMBINATION              0             20
  EXTERNAL                 3             51
  EXTERNAL BEAM            0             12
  IMPLANTS                 0              1
  INTERNAL                 0              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"
D32V22, binary
                cls
clus              0  1
  GAS6 MUTATED    0  0
  GAS6 WILD-TYPE 26  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0    0
  GAS6 WILD-TYPE   26    3
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  GAS6 MUTATED                    0                0                   1
  GAS6 WILD-TYPE                  2                2                  19
                vv
clus             REGIONAL SITE
  GAS6 MUTATED               0
  GAS6 WILD-TYPE             4
D32V23, multiclass
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             27 
    TCGA-C5-A0TN     TCGA-C5-A1BF     TCGA-C5-A2LZ     TCGA-C5-A7CK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DS-A7WF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A5FO     TCGA-EX-A3L1     TCGA-FU-A23L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A4S6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-JW-A5VG     TCGA-JX-A3Q0 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-R2-A69V     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V24, binary
                cls
clus              0  1
  GAS6 MUTATED    0  0
  GAS6 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0    0
  GAS6 WILD-TYPE   16    4
D32V25, continuous
D32V26, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2             99 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     TCGA-DS-A0VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HT 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A44S     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A449     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A770     TCGA-HG-A2PA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-IR-A3L7     TCGA-IR-A3LC     TCGA-IR-A3LF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V27, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2            108 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1BN     TCGA-C5-A1M5     TCGA-C5-A1M6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MQ     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2M2     TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A5RQ     TCGA-DS-A7WF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HQ     TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A411     TCGA-EA-A44S     TCGA-EA-A556     TCGA-EA-A5ZD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2IP     TCGA-EK-A2RK     TCGA-EX-A69L     TCGA-FU-A2QG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3TQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770     TCGA-HG-A2PA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-IR-A3L7     TCGA-IR-A3LC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V28, continuous
D32V29, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2            107 
    TCGA-BI-A0VS     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     TCGA-DS-A0VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A44S 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A556     TCGA-EA-A6QX     TCGA-EK-A2RN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H6     TCGA-EX-A449     TCGA-FU-A2QG     TCGA-FU-A3EO 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-IR-A3L7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A69B     TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-MU-A51Y 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V30, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2            101 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BE     TCGA-C5-A1BI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A1MP     TCGA-C5-A1MQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CH     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-C5-A7UE     TCGA-C5-A7UH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DR-A0ZL     TCGA-DS-A0VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HT 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A44S     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3HZ     TCGA-FU-A3TQ     TCGA-FU-A5XV     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JK     TCGA-IR-A3L7     TCGA-IR-A3LC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-Q1-A73Q     TCGA-RA-A741     TCGA-UC-A7PD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-UC-A7PF 
"GAS6 WILD-TYPE" 
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  GAS6 MUTATED                                     0
  GAS6 WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  GAS6 MUTATED                                     0                       0
  GAS6 WILD-TYPE                                   7                      28
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  GAS6 MUTATED                         0                       0
  GAS6 WILD-TYPE                       1                       6
D32V31, multiclass
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  GAS6 MUTATED                                               0
  GAS6 WILD-TYPE                                             2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  GAS6 MUTATED                                                1
  GAS6 WILD-TYPE                                              9
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  GAS6 MUTATED                                                                                   1
  GAS6 WILD-TYPE                                                                                59
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  GAS6 MUTATED                                                                                              2
  GAS6 WILD-TYPE                                                                                           86
D32V32, multiclass
                                                                                              clus
vv                                                                                             GAS6 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)                       1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)            2
                                                                                              clus
vv                                                                                             GAS6 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            9
  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"
D32V33, binary
                cls
clus              0  1
  GAS6 MUTATED    2  0
  GAS6 WILD-TYPE 61 67
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      2    0
  GAS6 WILD-TYPE   61   67
         clus
vv        GAS6 MUTATED GAS6 WILD-TYPE
  ABSENT             2             61
  PRESENT            0             67
[1] 2 2
[1] FALSE
D32V34, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1            120 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2M1     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-C5-A7UE     TCGA-DG-A2KH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3Y4 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B     TCGA-EA-A44S 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A6QX     TCGA-EK-A2RA     TCGA-EK-A2RO     TCGA-EK-A3GK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A40J     TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JX-A3PZ     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A7HU     TCGA-MU-A51Y 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A6DV     TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V35, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2            138 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MP     TCGA-C5-A1MQ     TCGA-C5-A2LS 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2M1     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-C5-A7UE     TCGA-DG-A2KH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VL 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A5FO     TCGA-EA-A6QX     TCGA-EK-A2GZ     TCGA-EK-A2IP 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2PK     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RC     TCGA-EK-A2RD     TCGA-EK-A2RE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RJ     TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EK-A2RN     TCGA-EK-A2RO     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A40J     TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JX-A3PZ     TCGA-JX-A3Q8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AV     TCGA-LP-A4AX     TCGA-LP-A5U2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A6DV     TCGA-Q1-A73P 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-UC-A7PF     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V36, binary
                cls
clus              0  1
  GAS6 MUTATED    2  2
  GAS6 WILD-TYPE 37 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      2    2
  GAS6 WILD-TYPE   37   84
                                          clus
vv                                         GAS6 MUTATED GAS6 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                2             37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            2             84
[1] 2 2
[1] FALSE
D32V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  GAS6 MUTATED              0           0          1
  GAS6 WILD-TYPE            8          43         45
D32V38, multiclass
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             1             96 
    TCGA-C5-A1BI     TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M6 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MN     TCGA-C5-A2LT     TCGA-C5-A2LV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A2M2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7UH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EK-A2R7     TCGA-EK-A3GK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JW-A69B     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-UC-A7PD     TCGA-WL-A834 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D32V39, continuous
D32V40, binary
                cls
clus              0  1
  GAS6 MUTATED    2  0
  GAS6 WILD-TYPE 86 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      2    0
  GAS6 WILD-TYPE   86   16
         clus
vv        GAS6 MUTATED GAS6 WILD-TYPE
  ABSENT             2             86
  PRESENT            0             16
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  GAS6 MUTATED             0         0     0
  GAS6 WILD-TYPE           2        16     1
D32V41, multiclass
D32V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  GAS6 MUTATED      0   1    0    1  0   0    0    0   0  0   0  0  1
  GAS6 WILD-TYPE    1  20   60   21  4   7    6   10  13  1   2  2  8
D32V43, multiclass
      clus
vv     GAS6 MUTATED GAS6 WILD-TYPE
  T1A1            0              1
  T1B             1             20
  T1B1            0             60
  T1B2            1             21
  T2              0              4
  T2A             0              7
  T2A1            0              6
  T2A2            0             10
  T2B             0             13
  T3              0              1
  T3B             0              2
  T4              0              2
  TX              1              8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  GAS6 MUTATED         0        1         0         0        0         0
  GAS6 WILD-TYPE       4        0         1         1       28        53
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  GAS6 MUTATED           2        0         0          0          0         0
  GAS6 WILD-TYPE        27        4         6          5          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  GAS6 MUTATED           0          1         0         0
  GAS6 WILD-TYPE         1         28         2         5
D32V45, multiclass
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1              0
  STAGE IA1             0              1
  STAGE IA2             0              1
  STAGE IB              0             28
  STAGE IB1             0             53
  STAGE IB2             2             27
  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(33) Variable = ABCD1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  ABCD1 MUTATED     4   3
  ABCD1 WILD-TYPE 146  37
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              7             183 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              3              37 
$`ABCD1 MUTATED`
TCGA-C5-A1BF TCGA-C5-A1MQ TCGA-DS-A0VK TCGA-EA-A3HU TCGA-EA-A411 TCGA-EK-A2R8 
       18.74        33.90        36.76        33.30        24.56         1.45 
TCGA-IR-A3LK 
       29.85 

$`ABCD1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        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        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       87.75        58.88         2.66       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-A3QD TCGA-EA-A3QE 
       12.36        37.35        30.90        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50        26.40        14.50        26.01        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51        19.27         0.43         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        47.77         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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-A3LL 
       66.81       117.40        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-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       195.85        30.31         7.99 
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 
       13.87        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        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  ABCD1 MUTATED ABCD1 WILD-TYPE 
           1.45            0.03 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
          36.76          210.67 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
          29.85           19.36 
[1] "1.4 - 36.8 (29.9)"  "0.0 - 210.7 (19.4)"
[1] "hr=" "2.4"
D33V2, continuous
                 vv
clus               T1  T2 T3+T4
  ABCD1 MUTATED     4   2     0
  ABCD1 WILD-TYPE 100  38     5
D33V3, multiclass
       clus
vv      ABCD1 MUTATED ABCD1 WILD-TYPE
  T1                4             100
  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"
D33V4, binary
                 cls
clus               0  1
  ABCD1 MUTATED    5  2
  ABCD1 WILD-TYPE 90 42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      5    2
  ABCD1 WILD-TYPE   90   42
   clus
vv  ABCD1 MUTATED ABCD1 WILD-TYPE
  0             5              90
  1             2              42
[1] 2 2
[1] FALSE
D33V5, binary
                 cls
clus               0  1
  ABCD1 MUTATED    5  0
  ABCD1 WILD-TYPE 74  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      5    0
  ABCD1 WILD-TYPE   74    4
   clus
vv  ABCD1 MUTATED ABCD1 WILD-TYPE
  0             5              74
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  ABCD1 MUTATED               0                                7
  ABCD1 WILD-TYPE             4                              151
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  ABCD1 MUTATED                                               0
  ABCD1 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  ABCD1 MUTATED                                     0
  ABCD1 WILD-TYPE                                  22
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  ABCD1 MUTATED                                           0
  ABCD1 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  ABCD1 MUTATED                                              0
  ABCD1 WILD-TYPE                                            3
D33V6, multiclass
                                               clus
vv                                              ABCD1 MUTATED ABCD1 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          7             151
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D33V7, binary
                 cls
clus                0   1
  ABCD1 MUTATED     2   5
  ABCD1 WILD-TYPE  30 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      2    5
  ABCD1 WILD-TYPE   30  157
     clus
vv    ABCD1 MUTATED ABCD1 WILD-TYPE
  NO              2              30
  YES             5             157
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "ABCD1 MUTATED"         
clus
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
D33V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCD1 MUTATED                                  0     0
  ABCD1 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ABCD1 MUTATED                           0
  ABCD1 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCD1 MUTATED                                           0     7
  ABCD1 WILD-TYPE                                         1   131
D33V10, multiclass
                                           clus
vv                                          ABCD1 MUTATED ABCD1 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                                                 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"
D33V11, binary
                 cls
clus                0   1
  ABCD1 MUTATED     0   5
  ABCD1 WILD-TYPE  14 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      0    5
  ABCD1 WILD-TYPE   14  129
                        clus
vv                       ABCD1 MUTATED ABCD1 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             5             129
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                 cls
clus               0  1
  ABCD1 MUTATED    3  2
  ABCD1 WILD-TYPE 94 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      3    2
  ABCD1 WILD-TYPE   94   29
            clus
vv           ABCD1 MUTATED ABCD1 WILD-TYPE
  TUMOR FREE             3              94
  WITH TUMOR             2              29
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  ABCD1 MUTATED        0      2       0             5       0
  ABCD1 WILD-TYPE      5      8       6           154      14
D33V14, multiclass
               clus
vv              ABCD1 MUTATED ABCD1 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    2               8
  UKRAINE                   0               6
  UNITED STATES             5             154
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  ABCD1 MUTATED    1  3  3  0  0
  ABCD1 WILD-TYPE 13 85 79  1  8
D33V15, multiclass
    clus
vv   ABCD1 MUTATED ABCD1 WILD-TYPE
  G1             1              13
  G2             3              85
  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"
D33V16, continuous
D33V17, continuous
[1] "Remove cluster labels:" "ABCD1 MUTATED"         
clus
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1ML 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2      TCGA-C5-A3HD 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DG-A2KL 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  ABCD1 MUTATED                                             1
  ABCD1 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  ABCD1 MUTATED                                        0
  ABCD1 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  ABCD1 MUTATED                                                 0
  ABCD1 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  ABCD1 MUTATED                1                   4
  ABCD1 WILD-TYPE             36                  89
D33V18, multiclass
                                                 clus
vv                                                ABCD1 MUTATED ABCD1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         4              89
[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"
D33V19, continuous
D33V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  ABCD1 MUTATED             2        1             1        0        0
  ABCD1 WILD-TYPE          18       53            11        1        7
D33V21, multiclass
               clus
vv              ABCD1 MUTATED ABCD1 WILD-TYPE
  COMBINATION               2              18
  EXTERNAL                  1              53
  EXTERNAL BEAM             1              11
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D33V22, binary
                 cls
clus               0  1
  ABCD1 MUTATED    2  0
  ABCD1 WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      2    0
  ABCD1 WILD-TYPE   24    3
                         clus
vv                        ABCD1 MUTATED ABCD1 WILD-TYPE
  COMPLETED AS PLANNED                2              24
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  ABCD1 MUTATED                    1                0                   0
  ABCD1 WILD-TYPE                  1                2                  20
                 vv
clus              REGIONAL SITE
  ABCD1 MUTATED               0
  ABCD1 WILD-TYPE             4
D33V23, multiclass
[1] "Remove cluster labels:" "ABCD1 MUTATED"         
clus
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BQ      TCGA-C5-A2LZ      TCGA-C5-A7CK 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DS-A7WF 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1      TCGA-FU-A23L 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
D33V24, binary
                 cls
clus               0  1
  ABCD1 MUTATED    0  0
  ABCD1 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      0    0
  ABCD1 WILD-TYPE   16    4
D33V25, continuous
D33V26, continuous
D33V27, continuous
D33V28, continuous
D33V29, continuous
D33V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  ABCD1 MUTATED                                     0
  ABCD1 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  ABCD1 MUTATED                                     2                       0
  ABCD1 WILD-TYPE                                   5                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  ABCD1 MUTATED                         0                       1
  ABCD1 WILD-TYPE                       1                       5
D33V31, multiclass
                                     clus
vv                                    ABCD1 MUTATED ABCD1 WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT             0               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT             2               5
  OTHER LOCATION, SPECIFY                         0              28
  POSITIVE BLADDER MARGIN                         0               1
  POSITIVE VAGINAL MARGIN                         1               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)
  ABCD1 MUTATED                                               0
  ABCD1 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  ABCD1 MUTATED                                                0
  ABCD1 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  ABCD1 MUTATED                                                                                   2
  ABCD1 WILD-TYPE                                                                                58
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  ABCD1 MUTATED                                                                                              3
  ABCD1 WILD-TYPE                                                                                           85
D33V32, multiclass
                                                                                              clus
vv                                                                                             ABCD1 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)             3
                                                                                              clus
vv                                                                                             ABCD1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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)              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"
D33V33, binary
                 cls
clus               0  1
  ABCD1 MUTATED    3  2
  ABCD1 WILD-TYPE 60 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      3    2
  ABCD1 WILD-TYPE   60   65
         clus
vv        ABCD1 MUTATED ABCD1 WILD-TYPE
  ABSENT              3              60
  PRESENT             2              65
[1] 2 2
[1] FALSE
D33V34, continuous
D33V35, continuous
D33V36, binary
                 cls
clus               0  1
  ABCD1 MUTATED    3  2
  ABCD1 WILD-TYPE 36 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      3    2
  ABCD1 WILD-TYPE   36   84
                                          clus
vv                                         ABCD1 MUTATED ABCD1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 3              36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             2              84
[1] 2 2
[1] FALSE
D33V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  ABCD1 MUTATED              0           1          3
  ABCD1 WILD-TYPE            8          42         43
D33V38, multiclass
              clus
vv             ABCD1 MUTATED ABCD1 WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              1              42
  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"
D33V39, continuous
D33V40, binary
                 cls
clus               0  1
  ABCD1 MUTATED    6  0
  ABCD1 WILD-TYPE 82 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      6    0
  ABCD1 WILD-TYPE   82   16
         clus
vv        ABCD1 MUTATED ABCD1 WILD-TYPE
  ABSENT              6              82
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  ABCD1 MUTATED             0         1     0
  ABCD1 WILD-TYPE           2        15     1
D33V41, multiclass
[1] "Remove cluster labels:" "ABCD1 MUTATED"         
clus
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A3HD 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"ABCD1 WILD-TYPE" "ABCD1 WILD-TYPE" 
D33V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  ABCD1 MUTATED      0   0    2    2  0   0    0    1   1  0   0  0  1
  ABCD1 WILD-TYPE    1  21   58   20  4   7    6    9  12  1   2  2  8
D33V43, multiclass
      clus
vv     ABCD1 MUTATED ABCD1 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             2              58
  T1B2             2              20
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             1               9
  T2B              1              12
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               1               8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  ABCD1 MUTATED         0        0         0         0        2         1
  ABCD1 WILD-TYPE       4        1         1         1       26        52
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  ABCD1 MUTATED           2        1         1          0          0         0
  ABCD1 WILD-TYPE        27        3         5          5          7        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  ABCD1 MUTATED           0          0         0         0
  ABCD1 WILD-TYPE         1         29         2         5
D33V45, multiclass
            clus
vv           ABCD1 MUTATED ABCD1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               2              26
  STAGE IB1              1              52
  STAGE IB2              2              27
  STAGE II               1               3
  STAGE IIA              1               5
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              0              14
  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(34) Variable = RPAP1 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  RPAP1 MUTATED     4   0
  RPAP1 WILD-TYPE 146  40
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              4             186 
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              0              40 
$`RPAP1 MUTATED`
TCGA-DR-A0ZM TCGA-JW-A5VL TCGA-MY-A5BD TCGA-Q1-A73O 
       58.88        15.58        54.81        14.07 

$`RPAP1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-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        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        40.04        87.75        36.76         2.66       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50        26.01        12.66        12.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       47.77         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84         0.92         2.17        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         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 
      117.40        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-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       195.85        30.31         7.99        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        13.87 
TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       34.62        35.05        20.84        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        9.04        16.14        17.56        15.88         9.34        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  RPAP1 MUTATED RPAP1 WILD-TYPE 
          14.07            0.03 
  RPAP1 MUTATED RPAP1 WILD-TYPE 
          58.88          210.67 
  RPAP1 MUTATED RPAP1 WILD-TYPE 
         35.195          19.690 
[1] "14.1 - 58.9 (35.2)" "0.0 - 210.7 (19.7)"
[1] "hr="     "2.5e+07"
D34V2, continuous
                 vv
clus               T1  T2 T3+T4
  RPAP1 MUTATED     1   2     0
  RPAP1 WILD-TYPE 103  38     5
D34V3, multiclass
       clus
vv      RPAP1 MUTATED RPAP1 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"
D34V4, binary
                 cls
clus               0  1
  RPAP1 MUTATED    2  0
  RPAP1 WILD-TYPE 93 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      2    0
  RPAP1 WILD-TYPE   93   44
   clus
vv  RPAP1 MUTATED RPAP1 WILD-TYPE
  0             2              93
  1             0              44
[1] 2 2
[1] FALSE
D34V5, binary
                 cls
clus               0  1
  RPAP1 MUTATED    2  0
  RPAP1 WILD-TYPE 77  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      2    0
  RPAP1 WILD-TYPE   77    4
   clus
vv  RPAP1 MUTATED RPAP1 WILD-TYPE
  0             2              77
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  RPAP1 MUTATED               0                                4
  RPAP1 WILD-TYPE             4                              154
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  RPAP1 MUTATED                                               0
  RPAP1 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  RPAP1 MUTATED                                     0
  RPAP1 WILD-TYPE                                  22
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  RPAP1 MUTATED                                           0
  RPAP1 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  RPAP1 MUTATED                                              0
  RPAP1 WILD-TYPE                                            3
D34V6, multiclass
                                               clus
vv                                              RPAP1 MUTATED RPAP1 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          4             154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D34V7, binary
                 cls
clus                0   1
  RPAP1 MUTATED     1   3
  RPAP1 WILD-TYPE  31 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      1    3
  RPAP1 WILD-TYPE   31  159
     clus
vv    RPAP1 MUTATED RPAP1 WILD-TYPE
  NO              1              31
  YES             3             159
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V9, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             119 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A410 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO      TCGA-EK-A3GK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPAP1 MUTATED                                  1     0
  RPAP1 WILD-TYPE                                7    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RPAP1 MUTATED                           0
  RPAP1 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPAP1 MUTATED                                           0     2
  RPAP1 WILD-TYPE                                         1   136
D34V10, multiclass
                                           clus
vv                                          RPAP1 MUTATED RPAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               7
  ASIAN                                                 0              19
  BLACK OR AFRICAN AMERICAN                             0              16
  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"
D34V11, binary
                 cls
clus                0   1
  RPAP1 MUTATED     3   1
  RPAP1 WILD-TYPE  11 133
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      3    1
  RPAP1 WILD-TYPE   11  133
                        clus
vv                       RPAP1 MUTATED RPAP1 WILD-TYPE
  HISPANIC OR LATINO                 3              11
  NOT HISPANIC OR LATINO             1             133
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                 cls
clus               0  1
  RPAP1 MUTATED    4  0
  RPAP1 WILD-TYPE 93 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      4    0
  RPAP1 WILD-TYPE   93   31
            clus
vv           RPAP1 MUTATED RPAP1 WILD-TYPE
  TUMOR FREE             4              93
  WITH TUMOR             0              31
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  RPAP1 MUTATED        0      0       0             4       0
  RPAP1 WILD-TYPE      5     10       6           155      14
D34V14, multiclass
               clus
vv              RPAP1 MUTATED RPAP1 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             4             155
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  RPAP1 MUTATED    2  1  0  0  1
  RPAP1 WILD-TYPE 12 87 82  1  7
D34V15, multiclass
    clus
vv   RPAP1 MUTATED RPAP1 WILD-TYPE
  G1             2              12
  G2             1              87
  G3             0              82
  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"
D34V16, continuous
D34V17, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              56 
     TCGA-BI-A0VR      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-EA-A556 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  RPAP1 MUTATED                                             0
  RPAP1 WILD-TYPE                                          26
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  RPAP1 MUTATED                                        0
  RPAP1 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  RPAP1 MUTATED                                                 0
  RPAP1 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  RPAP1 MUTATED                1                   3
  RPAP1 WILD-TYPE             36                  90
D34V18, multiclass
                                                 clus
vv                                                RPAP1 MUTATED RPAP1 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 0              26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              1              36
  LIFELONG NON-SMOKER                                         3              90
[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"
D34V19, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              51 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M7      TCGA-C5-A1ME 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LZ      TCGA-C5-A2M2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HF      TCGA-C5-A7CJ      TCGA-C5-A7CL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-DG-A2KK      TCGA-DS-A5RQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EK-A2RA      TCGA-EX-A1H5      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3TQ      TCGA-FU-A3TX 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A5XV      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LB 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-JW-A5VI      TCGA-JW-A5VK      TCGA-JX-A3Q0 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-Q1-A6DW      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  RPAP1 MUTATED             0        2             1        0        0
  RPAP1 WILD-TYPE          20       52            11        1        7
D34V21, multiclass
               clus
vv              RPAP1 MUTATED RPAP1 WILD-TYPE
  COMBINATION               0              20
  EXTERNAL                  2              52
  EXTERNAL BEAM             1              11
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D34V22, binary
                 cls
clus               0  1
  RPAP1 MUTATED    1  0
  RPAP1 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      1    0
  RPAP1 WILD-TYPE   25    3
                         clus
vv                        RPAP1 MUTATED RPAP1 WILD-TYPE
  COMPLETED AS PLANNED                1              25
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  RPAP1 MUTATED                    0                0                   0
  RPAP1 WILD-TYPE                  2                2                  20
                 vv
clus              REGIONAL SITE
  RPAP1 MUTATED               0
  RPAP1 WILD-TYPE             4
D34V23, multiclass
D34V24, binary
                 cls
clus               0  1
  RPAP1 MUTATED    0  0
  RPAP1 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      0    0
  RPAP1 WILD-TYPE   16    4
D34V25, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             163 
     TCGA-BI-A0VR      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1BQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MJ      TCGA-C5-A1MK      TCGA-C5-A1ML 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A439      TCGA-EA-A43B      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A5ZD      TCGA-EA-A5ZE      TCGA-EA-A5ZF      TCGA-EA-A6QX 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A78R      TCGA-EK-A2GZ      TCGA-EK-A2H0      TCGA-EK-A2IP 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2PL      TCGA-EK-A2PM      TCGA-EK-A2R7      TCGA-EK-A2R8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RC      TCGA-EK-A2RD      TCGA-EK-A2RJ      TCGA-EK-A2RK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RM      TCGA-EK-A2RN      TCGA-EK-A3GJ      TCGA-EK-A3GK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A3GM      TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A449      TCGA-EX-A69L      TCGA-EX-A69M      TCGA-FU-A23K 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A770      TCGA-HG-A2PA 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A69B      TCGA-JW-A852 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A4AU      TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A5U2      TCGA-LP-A5U3      TCGA-LP-A7HU      TCGA-Q1-A5R1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DV      TCGA-Q1-A6DW 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73Q      TCGA-Q1-A73S      TCGA-RA-A741 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V26, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1             100 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EX-A449      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-IR-A3L7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A69B 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V27, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             108 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M6      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A3HE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CO 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A5ZD      TCGA-EK-A2IP      TCGA-EK-A2RK      TCGA-EX-A69L 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A69B 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V28, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             167 
     TCGA-BI-A0VR      TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1BQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MJ      TCGA-C5-A1MK      TCGA-C5-A1ML 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LZ      TCGA-C5-A2M1      TCGA-C5-A2M2      TCGA-C5-A3HD 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KH      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A439      TCGA-EA-A43B      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A5ZD      TCGA-EA-A5ZE      TCGA-EA-A5ZF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EA-A78R      TCGA-EK-A2GZ      TCGA-EK-A2H0 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2IP      TCGA-EK-A2PL      TCGA-EK-A2PM      TCGA-EK-A2R7 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2R8      TCGA-EK-A2RC      TCGA-EK-A2RD      TCGA-EK-A2RJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RK      TCGA-EK-A2RM      TCGA-EK-A2RN      TCGA-EK-A3GJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A3GK      TCGA-EK-A3GM      TCGA-EX-A1H5      TCGA-EX-A1H6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A3L1      TCGA-EX-A449      TCGA-EX-A69L      TCGA-EX-A69M 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG      TCGA-FU-A3EO 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI      TCGA-FU-A3TQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A40J 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770      TCGA-HG-A2PA 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A69B      TCGA-JW-A852 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A4AU      TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A5U3      TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-Q1-A5R1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73P 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73Q      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V29, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1             108 
     TCGA-BI-A0VS      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A556      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EK-A2RN      TCGA-EX-A1H6      TCGA-EX-A449 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VK      TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-LP-A5U2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-MU-A51Y      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V30, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1             102 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A2M1 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EX-A69M      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A5XV      TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-Q1-A73Q      TCGA-RA-A741 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  RPAP1 MUTATED                                     0
  RPAP1 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  RPAP1 MUTATED                                     0                       1
  RPAP1 WILD-TYPE                                   7                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  RPAP1 MUTATED                         0                       0
  RPAP1 WILD-TYPE                       1                       6
D34V31, multiclass
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              43 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-UC-A7PD      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  RPAP1 MUTATED                                               0
  RPAP1 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  RPAP1 MUTATED                                                0
  RPAP1 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  RPAP1 MUTATED                                                                                   2
  RPAP1 WILD-TYPE                                                                                58
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  RPAP1 MUTATED                                                                                              2
  RPAP1 WILD-TYPE                                                                                           86
D34V32, multiclass
                                                                                              clus
vv                                                                                             RPAP1 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)             2
                                                                                              clus
vv                                                                                             RPAP1 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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)              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"
D34V33, binary
                 cls
clus               0  1
  RPAP1 MUTATED    1  2
  RPAP1 WILD-TYPE 62 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      1    2
  RPAP1 WILD-TYPE   62   65
         clus
vv        RPAP1 MUTATED RPAP1 WILD-TYPE
  ABSENT              1              62
  PRESENT             2              65
[1] 2 2
[1] FALSE
D34V34, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             119 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A410 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO      TCGA-EK-A3GK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V35, continuous
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              2             138 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2GZ      TCGA-EK-A2IP 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2PK      TCGA-EK-A2R7      TCGA-EK-A2R8      TCGA-EK-A2R9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EK-A2RC      TCGA-EK-A2RD      TCGA-EK-A2RE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RJ      TCGA-EK-A2RK      TCGA-EK-A2RL      TCGA-EK-A2RM 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EK-A3GJ      TCGA-EK-A3GK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-MU-A5YI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV      TCGA-Q1-A73P 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-UC-A7PD 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-UC-A7PF      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V36, binary
                 cls
clus               0  1
  RPAP1 MUTATED    0  3
  RPAP1 WILD-TYPE 39 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      0    3
  RPAP1 WILD-TYPE   39   83
                                          clus
vv                                         RPAP1 MUTATED RPAP1 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 0              39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             3              83
[1] 2 2
[1] FALSE
D34V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  RPAP1 MUTATED              0           1          0
  RPAP1 WILD-TYPE            8          42         46
D34V38, multiclass
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              96 
     TCGA-C5-A1BI      TCGA-C5-A1BL      TCGA-C5-A1BN      TCGA-C5-A1M6 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MN      TCGA-C5-A2LT      TCGA-C5-A2LV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7UH 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KM      TCGA-DR-A0ZL      TCGA-DS-A0VK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5O9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EA-A5ZE      TCGA-EA-A5ZF      TCGA-EK-A2R7      TCGA-EK-A3GK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A1H5      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A5U2      TCGA-LP-A5U3      TCGA-LP-A7HU 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A5R1      TCGA-Q1-A5R2      TCGA-Q1-A5R3      TCGA-Q1-A6DV 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-UC-A7PD      TCGA-WL-A834 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V39, continuous
D34V40, binary
                 cls
clus               0  1
  RPAP1 MUTATED    1  2
  RPAP1 WILD-TYPE 87 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP1 MUTATED      1    2
  RPAP1 WILD-TYPE   87   14
         clus
vv        RPAP1 MUTATED RPAP1 WILD-TYPE
  ABSENT              1              87
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  RPAP1 MUTATED             0         1     0
  RPAP1 WILD-TYPE           2        15     1
D34V41, multiclass
[1] "Remove cluster labels:" "RPAP1 MUTATED"         
clus
  RPAP1 MUTATED RPAP1 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"RPAP1 WILD-TYPE" "RPAP1 WILD-TYPE" 
D34V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  RPAP1 MUTATED      0   0    0    1  0   0    0    0   2  0   0  0  1
  RPAP1 WILD-TYPE    1  21   60   21  4   7    6   10  11  1   2  2  8
D34V43, multiclass
      clus
vv     RPAP1 MUTATED RPAP1 WILD-TYPE
  T1A1             0               1
  T1B              0              21
  T1B1             0              60
  T1B2             1              21
  T2               0               4
  T2A              0               7
  T2A1             0               6
  T2A2             0              10
  T2B              2              11
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               1               8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  RPAP1 MUTATED         0        0         0         0        0         0
  RPAP1 WILD-TYPE       4        1         1         1       28        53
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  RPAP1 MUTATED           2        0         0          0          0         1
  RPAP1 WILD-TYPE        27        4         6          5          7        13
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  RPAP1 MUTATED           0          1         0         0
  RPAP1 WILD-TYPE         1         28         2         5
D34V45, multiclass
            clus
vv           RPAP1 MUTATED RPAP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               0              28
  STAGE IB1              0              53
  STAGE IB2              2              27
  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              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(35) Variable = HIST1H4E MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  HIST1H4E MUTATED     3   1
  HIST1H4E WILD-TYPE 147  39
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 4                186 
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 1                 39 
$`HIST1H4E MUTATED`
TCGA-C5-A1BN TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-FU-A5XV 
        5.46        44.94        58.88         1.97 

$`HIST1H4E WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       40.93         3.58        33.90        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        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-A2KM 
      131.11         9.34         1.12        58.88        50.76        40.04 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       87.75        36.76         2.66       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 
       12.36        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        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
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       117.40        96.95        78.71 
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-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       21.44        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 
      195.85        30.31         7.99        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        13.87        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        15.39 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.36        19.59         3.88        11.67        93.99        26.01 

  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
              1.97               0.03 
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
             58.88             210.67 
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
             25.20              19.69 
[1] "2.0 - 58.9 (25.2)"  "0.0 - 210.7 (19.7)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                  T1  T2 T3+T4
  HIST1H4E MUTATED     1   2     0
  HIST1H4E WILD-TYPE 103  38     5
D35V3, multiclass
       clus
vv      HIST1H4E MUTATED HIST1H4E 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"
D35V4, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    2  1
  HIST1H4E WILD-TYPE 93 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      2    1
  HIST1H4E WILD-TYPE   93   43
   clus
vv  HIST1H4E MUTATED HIST1H4E WILD-TYPE
  0                2                 93
  1                1                 43
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    2  0
  HIST1H4E WILD-TYPE 77  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      2    0
  HIST1H4E WILD-TYPE   77    4
   clus
vv  HIST1H4E MUTATED HIST1H4E WILD-TYPE
  0                2                 77
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  HIST1H4E MUTATED               0                                4
  HIST1H4E WILD-TYPE             4                              154
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  HIST1H4E MUTATED                                               0
  HIST1H4E WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  HIST1H4E MUTATED                                     0
  HIST1H4E WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  HIST1H4E MUTATED                                           0
  HIST1H4E WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  HIST1H4E MUTATED                                              0
  HIST1H4E WILD-TYPE                                            3
D35V6, multiclass
                                               clus
vv                                              HIST1H4E 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                                              HIST1H4E WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   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"
D35V7, binary
                    cls
clus                   0   1
  HIST1H4E MUTATED     2   2
  HIST1H4E WILD-TYPE  30 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      2    2
  HIST1H4E WILD-TYPE   30  160
     clus
vv    HIST1H4E MUTATED HIST1H4E WILD-TYPE
  NO                 2                 30
  YES                2                160
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H4E MUTATED                                  0     0
  HIST1H4E WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  HIST1H4E MUTATED                           0
  HIST1H4E WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIST1H4E MUTATED                                           0     3
  HIST1H4E WILD-TYPE                                         1   135
D35V10, multiclass
                                           clus
vv                                          HIST1H4E MUTATED HIST1H4E 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                                                    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"
D35V11, binary
                    cls
clus                   0   1
  HIST1H4E MUTATED     0   3
  HIST1H4E WILD-TYPE  14 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      0    3
  HIST1H4E WILD-TYPE   14  131
                        clus
vv                       HIST1H4E MUTATED HIST1H4E WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO                3                131
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    2  1
  HIST1H4E WILD-TYPE 95 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      2    1
  HIST1H4E WILD-TYPE   95   30
            clus
vv           HIST1H4E MUTATED HIST1H4E WILD-TYPE
  TUMOR FREE                2                 95
  WITH TUMOR                1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  HIST1H4E MUTATED        1      0       0             3       0
  HIST1H4E WILD-TYPE      4     10       6           156      14
D35V14, multiclass
               clus
vv              HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CANADA                       1                  4
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                3                156
  VIETNAM                      0                 14
[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                 G1 G2 G3 G4 GX
  HIST1H4E MUTATED    1  1  2  0  0
  HIST1H4E WILD-TYPE 13 87 80  1  8
D35V15, multiclass
    clus
vv   HIST1H4E MUTATED HIST1H4E WILD-TYPE
  G1                1                 13
  G2                1                 87
  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"
D35V16, continuous
D35V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  HIST1H4E MUTATED                                             0
  HIST1H4E WILD-TYPE                                          26
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  HIST1H4E MUTATED                                        0
  HIST1H4E WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  HIST1H4E MUTATED                                                 0
  HIST1H4E WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  HIST1H4E MUTATED                4                   0
  HIST1H4E WILD-TYPE             33                  93
D35V18, multiclass
                                                 clus
vv                                                HIST1H4E MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            0
                                                 clus
vv                                                HIST1H4E WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             93
[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"
D35V19, continuous
D35V20, continuous
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                 80 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M8         TCGA-C5-A1M9 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MQ         TCGA-C5-A2LT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7UE         TCGA-C5-A7UH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DG-A2KJ         TCGA-DG-A2KK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DG-A2KM         TCGA-DS-A0VK         TCGA-DS-A0VN 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A3QD 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A43B         TCGA-EA-A44S 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A5FO         TCGA-EA-A5O9 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EK-A2H0         TCGA-EX-A3L1         TCGA-EX-A449 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK         TCGA-HM-A4S6 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JW-A5VG         TCGA-JW-A5VH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JX-A5QV         TCGA-LP-A4AU 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-LP-A4AX         TCGA-LP-A7HU         TCGA-MU-A5YI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-MY-A5BD         TCGA-MY-A5BF         TCGA-Q1-A5R2 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-Q1-A6DW         TCGA-Q1-A73O 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-R2-A69V 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-RA-A741         TCGA-WL-A834 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  HIST1H4E MUTATED             1        1             1        0        0
  HIST1H4E WILD-TYPE          19       53            11        1        7
D35V21, multiclass
               clus
vv              HIST1H4E MUTATED HIST1H4E WILD-TYPE
  COMBINATION                  1                 19
  EXTERNAL                     1                 53
  EXTERNAL BEAM                1                 11
  IMPLANTS                     0                  1
  INTERNAL                     0                  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"
D35V22, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    2  0
  HIST1H4E WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      2    0
  HIST1H4E WILD-TYPE   24    3
                         clus
vv                        HIST1H4E MUTATED HIST1H4E WILD-TYPE
  COMPLETED AS PLANNED                   2                 24
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  HIST1H4E MUTATED                    0                0                   1
  HIST1H4E WILD-TYPE                  2                2                  19
                    vv
clus                 REGIONAL SITE
  HIST1H4E MUTATED               0
  HIST1H4E WILD-TYPE             4
D35V23, multiclass
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 1                 27 
        TCGA-C5-A0TN         TCGA-C5-A1BF         TCGA-C5-A1BQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A7UE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DS-A7WF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EA-A5FO         TCGA-EX-A3L1 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A4S6         TCGA-IR-A3LF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VG         TCGA-JX-A3Q0 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-R2-A69V         TCGA-WL-A834 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
D35V24, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    1  0
  HIST1H4E WILD-TYPE 15  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      1    0
  HIST1H4E WILD-TYPE   15    4
     clus
vv    HIST1H4E MUTATED HIST1H4E WILD-TYPE
  CGY                1                 15
  GY                 0                  4
[1] 2 2
[1] FALSE
D35V25, continuous
D35V26, continuous
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                 99 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         TCGA-C5-A1ML 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-C5-A1MQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HT         TCGA-EA-A3HU 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EX-A449 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3TQ         TCGA-FU-A770 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-IR-A3L7 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
D35V27, continuous
D35V28, continuous
D35V29, continuous
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                107 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         TCGA-C5-A1ML 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-C5-A1MQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3HU         TCGA-EA-A3QD         TCGA-EA-A3QE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A556 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A6QX         TCGA-EK-A2RN 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EX-A1H6         TCGA-EX-A449         TCGA-FU-A2QG 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A770         TCGA-HG-A2PA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK         TCGA-IR-A3L7 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-MU-A51Y         TCGA-RA-A741 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
D35V30, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  HIST1H4E MUTATED                                     0
  HIST1H4E WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  HIST1H4E MUTATED                                     0
  HIST1H4E WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  HIST1H4E MUTATED                         1                       0
  HIST1H4E WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  HIST1H4E MUTATED                         1
  HIST1H4E WILD-TYPE                       5
D35V31, multiclass
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                 42 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BM         TCGA-C5-A1M5 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MJ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A1MQ         TCGA-C5-A2LS 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A3HE         TCGA-C5-A3HL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CJ         TCGA-C5-A7UC 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A1OA         TCGA-DS-A3LQ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-UC-A7PD         TCGA-WL-A834 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  HIST1H4E MUTATED                                               0
  HIST1H4E WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  HIST1H4E MUTATED                                                0
  HIST1H4E WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  HIST1H4E MUTATED                                                                                   2
  HIST1H4E WILD-TYPE                                                                                58
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  HIST1H4E MUTATED                                                                                              2
  HIST1H4E WILD-TYPE                                                                                           86
D35V32, multiclass
                                                                                              clus
vv                                                                                             HIST1H4E 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)                2
                                                                                              clus
vv                                                                                             HIST1H4E WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  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)                 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"
D35V33, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    0  4
  HIST1H4E WILD-TYPE 63 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      0    4
  HIST1H4E WILD-TYPE   63   63
         clus
vv        HIST1H4E MUTATED HIST1H4E WILD-TYPE
  ABSENT                 0                 63
  PRESENT                4                 63
[1] 2 2
[1] FALSE
D35V34, continuous
D35V35, continuous
D35V36, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    1  2
  HIST1H4E WILD-TYPE 38 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      1    2
  HIST1H4E WILD-TYPE   38   84
                                          clus
vv                                         HIST1H4E MUTATED HIST1H4E WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                2                 84
[1] 2 2
[1] FALSE
D35V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  HIST1H4E MUTATED              0           1          1
  HIST1H4E WILD-TYPE            8          42         45
D35V38, multiclass
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                 95 
        TCGA-C5-A1BI         TCGA-C5-A1BL         TCGA-C5-A1M6 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MN 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-C5-A2M1         TCGA-C5-A2M2 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HL         TCGA-C5-A7CG 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-DG-A2KM 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A1OA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A3HU         TCGA-EA-A3QD         TCGA-EA-A3QE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A43B 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EA-A5ZE 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EA-A5ZF         TCGA-EK-A2R7         TCGA-EK-A3GK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EX-A69L         TCGA-EX-A69M         TCGA-FU-A2QG 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3WB 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A57G         TCGA-FU-A770 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK         TCGA-HM-A4S6 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LA 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A69B         TCGA-JX-A3PZ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-LP-A5U2         TCGA-LP-A5U3         TCGA-LP-A7HU 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A5R2         TCGA-Q1-A5R3 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-WL-A834 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
D35V39, continuous
D35V40, binary
                    cls
clus                  0  1
  HIST1H4E MUTATED    1  1
  HIST1H4E WILD-TYPE 87 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4E MUTATED      1    1
  HIST1H4E WILD-TYPE   87   15
         clus
vv        HIST1H4E MUTATED HIST1H4E WILD-TYPE
  ABSENT                 1                 87
  PRESENT                1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  HIST1H4E MUTATED             0         2     0
  HIST1H4E WILD-TYPE           2        14     1
D35V41, multiclass
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 2                 17 
        TCGA-C5-A1BE         TCGA-C5-A1BI         TCGA-C5-A1M9 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MQ         TCGA-C5-A2LT 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A3HD 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-DS-A1OA         TCGA-DS-A3LQ         TCGA-EK-A2H0 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-EK-A2H1         TCGA-HM-A3JJ 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
D35V42, continuous
[1] "Remove cluster labels:" "HIST1H4E MUTATED"      
clus
  HIST1H4E MUTATED HIST1H4E WILD-TYPE 
                 1                  9 
        TCGA-C5-A1MH         TCGA-C5-A1ML         TCGA-C5-A1MN 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-HM-A3JK 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MU-A51Y 
"HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" "HIST1H4E WILD-TYPE" 
                    vv
clus                 T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  HIST1H4E MUTATED      0   0    0    1  0   1    0    0   1  0   0  0  0
  HIST1H4E WILD-TYPE    1  21   60   21  4   6    6   10  12  1   2  2  9
D35V43, multiclass
      clus
vv     HIST1H4E MUTATED HIST1H4E WILD-TYPE
  T1A1                0                  1
  T1B                 0                 21
  T1B1                0                 60
  T1B2                1                 21
  T2                  0                  4
  T2A                 1                  6
  T2A1                0                  6
  T2A2                0                 10
  T2B                 1                 12
  T3                  0                  1
  T3B                 0                  2
  T4                  0                  2
  TX                  0                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V44, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  HIST1H4E MUTATED         0        0         0         0        0         0
  HIST1H4E WILD-TYPE       4        1         1         1       28        53
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  HIST1H4E MUTATED           1        0         1          0          0
  HIST1H4E WILD-TYPE        28        4         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  HIST1H4E MUTATED           0         0          2         0         0
  HIST1H4E WILD-TYPE        14         1         27         2         5
D35V45, multiclass
            clus
vv           HIST1H4E MUTATED HIST1H4E WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 28
  STAGE IB1                 0                 53
  STAGE IB2                 1                 28
  STAGE II                  0                  4
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  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(36) Variable = NLRC5 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  NLRC5 MUTATED     6   1
  NLRC5 WILD-TYPE 144  39
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             183 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              1              39 
$`NLRC5 MUTATED`
TCGA-DS-A0VL TCGA-EA-A439 TCGA-EK-A3GK TCGA-FU-A3HZ TCGA-IR-A3LK TCGA-JW-A5VL 
        2.66        14.50         0.10        36.26        29.85        15.58 
TCGA-Q1-A73P 
       15.88 

$`NLRC5 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-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        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       44.94        40.04        87.75        58.88        36.76       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        12.36        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        14.50        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        45.96        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        47.77 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         0.92         2.17        31.36         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       20.48        28.37         8.28        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        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        13.87        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-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07         9.34        15.39        19.36        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       11.67        93.99        26.01 

  NLRC5 MUTATED NLRC5 WILD-TYPE 
           0.10            0.03 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
          36.26          210.67 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
          15.58           19.86 
[1] "0.1 - 36.3 (15.6)"  "0.0 - 210.7 (19.9)"
[1] "hr=" "1.3"
D36V2, continuous
                 vv
clus              T1 T2 T3+T4
  NLRC5 MUTATED    5  2     0
  NLRC5 WILD-TYPE 99 38     5
D36V3, multiclass
       clus
vv      NLRC5 MUTATED NLRC5 WILD-TYPE
  T1                5              99
  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"
D36V4, binary
                 cls
clus               0  1
  NLRC5 MUTATED    6  0
  NLRC5 WILD-TYPE 89 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      6    0
  NLRC5 WILD-TYPE   89   44
   clus
vv  NLRC5 MUTATED NLRC5 WILD-TYPE
  0             6              89
  1             0              44
[1] 2 2
[1] FALSE
D36V5, binary
                 cls
clus               0  1
  NLRC5 MUTATED    4  0
  NLRC5 WILD-TYPE 75  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      4    0
  NLRC5 WILD-TYPE   75    4
   clus
vv  NLRC5 MUTATED NLRC5 WILD-TYPE
  0             4              75
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  NLRC5 MUTATED               0                                5
  NLRC5 WILD-TYPE             4                              153
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  NLRC5 MUTATED                                               0
  NLRC5 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  NLRC5 MUTATED                                     2
  NLRC5 WILD-TYPE                                  20
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  NLRC5 MUTATED                                           0
  NLRC5 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  NLRC5 MUTATED                                              0
  NLRC5 WILD-TYPE                                            3
D36V6, multiclass
                                               clus
vv                                              NLRC5 MUTATED NLRC5 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          5             153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       2              20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D36V7, binary
                 cls
clus                0   1
  NLRC5 MUTATED     0   7
  NLRC5 WILD-TYPE  32 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      0    7
  NLRC5 WILD-TYPE   32  155
     clus
vv    NLRC5 MUTATED NLRC5 WILD-TYPE
  NO              0              32
  YES             7             155
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRC5 MUTATED                                  1     1
  NLRC5 WILD-TYPE                                7    18
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NLRC5 MUTATED                           0
  NLRC5 WILD-TYPE                        16
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NLRC5 MUTATED                                           0     5
  NLRC5 WILD-TYPE                                         1   133
D36V10, multiclass
                                           clus
vv                                          NLRC5 MUTATED NLRC5 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                                                 5             133
[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"
D36V11, binary
                 cls
clus                0   1
  NLRC5 MUTATED     1   4
  NLRC5 WILD-TYPE  13 130
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      1    4
  NLRC5 WILD-TYPE   13  130
                        clus
vv                       NLRC5 MUTATED NLRC5 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             4             130
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                 cls
clus               0  1
  NLRC5 MUTATED    4  1
  NLRC5 WILD-TYPE 93 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      4    1
  NLRC5 WILD-TYPE   93   30
            clus
vv           NLRC5 MUTATED NLRC5 WILD-TYPE
  TUMOR FREE             4              93
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  NLRC5 MUTATED        0      0       0             6       1
  NLRC5 WILD-TYPE      5     10       6           153      13
D36V14, multiclass
               clus
vv              NLRC5 MUTATED NLRC5 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             6             153
  VIETNAM                   1              13
[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              G1 G2 G3 G4 GX
  NLRC5 MUTATED    2  1  4  0  0
  NLRC5 WILD-TYPE 12 87 78  1  8
D36V15, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  G1             2              12
  G2             1              87
  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"
D36V16, continuous
D36V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  NLRC5 MUTATED                                             0
  NLRC5 WILD-TYPE                                          26
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  NLRC5 MUTATED                                        0
  NLRC5 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  NLRC5 MUTATED                                                 0
  NLRC5 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  NLRC5 MUTATED                0                   6
  NLRC5 WILD-TYPE             37                  87
D36V18, multiclass
                                                 clus
vv                                                NLRC5 MUTATED NLRC5 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 0              26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              0              37
  LIFELONG NON-SMOKER                                         6              87
[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"
D36V19, continuous
D36V20, continuous
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              2              80 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1M6      TCGA-C5-A1M8 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1ML      TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A2LY      TCGA-C5-A2LZ      TCGA-C5-A3HD      TCGA-C5-A3HF 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7UE      TCGA-C5-A7UH 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DG-A2KM      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VN 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WH 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A3QD      TCGA-EA-A3Y4      TCGA-EA-A43B 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A5FO      TCGA-EA-A5O9 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EK-A2H0      TCGA-EX-A3L1      TCGA-EX-A449      TCGA-FU-A23L 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AU      TCGA-LP-A4AX      TCGA-LP-A7HU 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R2 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-Q1-A5R3      TCGA-Q1-A6DW      TCGA-Q1-A73O      TCGA-Q1-A73Q 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741      TCGA-WL-A834 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  NLRC5 MUTATED             0        2             0        0        0
  NLRC5 WILD-TYPE          20       52            12        1        7
D36V21, multiclass
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              2              92 
     TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6      TCGA-C5-A1M8 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MQ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2LZ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A3HD      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KJ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZM 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A3QD 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EA-A5FO      TCGA-EA-A5O9      TCGA-EK-A2H0      TCGA-EX-A3L1 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EX-A449      TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-HM-A3JJ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC      TCGA-IR-A3LF 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LL      TCGA-JW-A5VG 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JX-A3Q0      TCGA-JX-A5QV 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LP-A4AU      TCGA-LP-A4AX      TCGA-LP-A7HU      TCGA-MU-A5YI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R2      TCGA-Q1-A5R3 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-Q1-A6DW      TCGA-Q1-A73O      TCGA-Q1-A73Q      TCGA-Q1-A73S 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-R2-A69V      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-WL-A834 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
D36V22, binary
                 cls
clus               0  1
  NLRC5 MUTATED    0  0
  NLRC5 WILD-TYPE 26  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      0    0
  NLRC5 WILD-TYPE   26    3
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  NLRC5 MUTATED                    0                0                   1
  NLRC5 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  NLRC5 MUTATED               0
  NLRC5 WILD-TYPE             4
D36V23, multiclass
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A2LZ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7CK      TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A3HY      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
D36V24, binary
                 cls
clus               0  1
  NLRC5 MUTATED    1  0
  NLRC5 WILD-TYPE 15  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      1    0
  NLRC5 WILD-TYPE   15    4
     clus
vv    NLRC5 MUTATED NLRC5 WILD-TYPE
  CGY             1              15
  GY              0               4
[1] 2 2
[1] FALSE
D36V25, continuous
D36V26, continuous
D36V27, continuous
D36V28, continuous
D36V29, continuous
D36V30, continuous
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  NLRC5 MUTATED                                     0
  NLRC5 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  NLRC5 MUTATED                                     1                       1
  NLRC5 WILD-TYPE                                   6                      27
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  NLRC5 MUTATED                         0                       0
  NLRC5 WILD-TYPE                       1                       6
D36V31, multiclass
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              2              42 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VM 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EA-A50E 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A1H5      TCGA-EX-A449 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-WL-A834 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  NLRC5 MUTATED                                               0
  NLRC5 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  NLRC5 MUTATED                                                0
  NLRC5 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  NLRC5 MUTATED                                                                                   2
  NLRC5 WILD-TYPE                                                                                58
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  NLRC5 MUTATED                                                                                              4
  NLRC5 WILD-TYPE                                                                                           84
D36V32, multiclass
                                                                                              clus
vv                                                                                             NLRC5 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)             4
                                                                                              clus
vv                                                                                             NLRC5 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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)              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"
D36V33, binary
                 cls
clus               0  1
  NLRC5 MUTATED    1  4
  NLRC5 WILD-TYPE 62 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      1    4
  NLRC5 WILD-TYPE   62   63
         clus
vv        NLRC5 MUTATED NLRC5 WILD-TYPE
  ABSENT              1              62
  PRESENT             4              63
[1] 2 2
[1] FALSE
D36V34, continuous
D36V35, continuous
D36V36, binary
                 cls
clus               0  1
  NLRC5 MUTATED    0  4
  NLRC5 WILD-TYPE 39 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      0    4
  NLRC5 WILD-TYPE   39   82
                                          clus
vv                                         NLRC5 MUTATED NLRC5 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 0              39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             4              82
[1] 2 2
[1] FALSE
D36V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  NLRC5 MUTATED              1           1          2
  NLRC5 WILD-TYPE            7          42         44
D36V38, multiclass
              clus
vv             NLRC5 MUTATED NLRC5 WILD-TYPE
  CURRENT USER             1               7
  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"
D36V39, continuous
D36V40, binary
                 cls
clus               0  1
  NLRC5 MUTATED    4  2
  NLRC5 WILD-TYPE 84 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      4    2
  NLRC5 WILD-TYPE   84   14
         clus
vv        NLRC5 MUTATED NLRC5 WILD-TYPE
  ABSENT              4              84
  PRESENT             2              14
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  NLRC5 MUTATED             0         0     0
  NLRC5 WILD-TYPE           2        16     1
D36V41, multiclass
D36V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  NLRC5 MUTATED      0   1    2    2  0   0    1    1   0  0   0  0  0
  NLRC5 WILD-TYPE    1  20   58   20  4   7    5    9  13  1   2  2  9
D36V43, multiclass
      clus
vv     NLRC5 MUTATED NLRC5 WILD-TYPE
  T1A1             0               1
  T1B              1              20
  T1B1             2              58
  T1B2             2              20
  T2               0               4
  T2A              0               7
  T2A1             1               5
  T2A2             1               9
  T2B              0              13
  T3               0               1
  T3B              0               2
  T4               0               2
  TX               0               9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  NLRC5 MUTATED         0        0         0         0        1         2
  NLRC5 WILD-TYPE       4        1         1         1       27        51
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  NLRC5 MUTATED           2        0         0          1          1         0
  NLRC5 WILD-TYPE        27        4         6          4          6        14
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  NLRC5 MUTATED           0          0         0         0
  NLRC5 WILD-TYPE         1         29         2         5
D36V45, multiclass
            clus
vv           NLRC5 MUTATED NLRC5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               1              27
  STAGE IB1              2              51
  STAGE IB2              2              27
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             1               4
  STAGE IIA2             1               6
  STAGE IIB              0              14
  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(37) Variable = DDX41 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  DDX41 MUTATED     4   1
  DDX41 WILD-TYPE 146  39
  DDX41 MUTATED DDX41 WILD-TYPE 
              5             185 
  DDX41 MUTATED DDX41 WILD-TYPE 
              1              39 
$`DDX41 MUTATED`
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-EK-A2PG TCGA-EX-A1H5 TCGA-Q1-A5R2 
      100.14        52.01         1.51        20.35        16.41 

$`DDX41 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-A3HE 
       73.45        83.05        78.35        38.43        33.24        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        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       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        12.36        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        14.50        26.40        24.56        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01        12.66        12.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL 
       12.59        45.96        26.27         6.64        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17        31.36        36.26         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
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       117.40        96.95        78.71 
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-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ 
       21.44        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 
      195.85        30.31         7.99        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        13.87        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-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        15.39        19.36 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-WL-A834 
       19.59         3.88        11.67        93.99        26.01 

  DDX41 MUTATED DDX41 WILD-TYPE 
           1.51            0.03 
  DDX41 MUTATED DDX41 WILD-TYPE 
         100.14          210.67 
  DDX41 MUTATED DDX41 WILD-TYPE 
          20.35           19.59 
[1] "1.5 - 100.1 (20.4)" "0.0 - 210.7 (19.6)"
[1] "hr=" "1.3"
D37V2, continuous
                 vv
clus               T1  T2 T3+T4
  DDX41 MUTATED     0   1     0
  DDX41 WILD-TYPE 104  39     5
D37V3, multiclass
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1             148 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BK      TCGA-C5-A1BM      TCGA-C5-A1M5 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MJ      TCGA-C5-A1MP 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A3HE 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KH      TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KM      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A439      TCGA-EA-A43B      TCGA-EA-A44S      TCGA-EA-A4BA 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO      TCGA-EA-A5O9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A5ZD      TCGA-EA-A5ZE      TCGA-EA-A5ZF      TCGA-EA-A6QX 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A78R      TCGA-EK-A2IP      TCGA-EK-A2R7      TCGA-EK-A2R8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2R9      TCGA-EK-A2RA      TCGA-EK-A2RD      TCGA-EK-A2RE 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RJ      TCGA-EK-A2RK      TCGA-EK-A2RL      TCGA-EK-A2RN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A3GJ      TCGA-EK-A3GK      TCGA-EX-A1H6      TCGA-EX-A3L1 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A449      TCGA-EX-A69L      TCGA-EX-A69M      TCGA-FU-A23K 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A23L      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-FU-A3NI      TCGA-FU-A3TQ      TCGA-FU-A3TX 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-FU-A3YQ      TCGA-FU-A40J      TCGA-FU-A57G 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A5XV      TCGA-FU-A770      TCGA-HG-A2PA      TCGA-HM-A3JJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-HM-A6W2      TCGA-IR-A3L7 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC      TCGA-IR-A3LF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A4AU      TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A5U2      TCGA-LP-A5U3      TCGA-LP-A7HU      TCGA-MU-A51Y 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BE      TCGA-MY-A5BF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A5R1      TCGA-Q1-A6DV      TCGA-Q1-A73P      TCGA-Q1-A73S 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-R2-A69V      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V4, binary
                 cls
clus               0  1
  DDX41 MUTATED    0  1
  DDX41 WILD-TYPE 95 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      0    1
  DDX41 WILD-TYPE   95   43
   clus
vv  DDX41 MUTATED DDX41 WILD-TYPE
  0             0              95
  1             1              43
[1] 2 2
[1] FALSE
D37V5, binary
                 cls
clus               0  1
  DDX41 MUTATED    0  0
  DDX41 WILD-TYPE 79  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      0    0
  DDX41 WILD-TYPE   79    4
                 vv
clus              ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DDX41 MUTATED               0                                5
  DDX41 WILD-TYPE             4                              153
                 vv
clus              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DDX41 MUTATED                                               0
  DDX41 WILD-TYPE                                             5
                 vv
clus              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DDX41 MUTATED                                     0
  DDX41 WILD-TYPE                                  22
                 vv
clus              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DDX41 MUTATED                                           0
  DDX41 WILD-TYPE                                         2
                 vv
clus              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DDX41 MUTATED                                              0
  DDX41 WILD-TYPE                                            3
D37V6, multiclass
                                               clus
vv                                              DDX41 MUTATED DDX41 WILD-TYPE
  ADENOSQUAMOUS                                             0               4
  CERVICAL SQUAMOUS CELL CARCINOMA                          5             153
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE             0               5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                       0              22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                 0               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE              0               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"
D37V7, binary
                 cls
clus                0   1
  DDX41 MUTATED     2   3
  DDX41 WILD-TYPE  30 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      2    3
  DDX41 WILD-TYPE   30  159
     clus
vv    DDX41 MUTATED DDX41 WILD-TYPE
  NO              2              30
  YES             3             159
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1             120 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A3GK      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R1 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A6DV      TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX41 MUTATED                                  0     0
  DDX41 WILD-TYPE                                8    19
                 vv
clus              BLACK OR AFRICAN AMERICAN
  DDX41 MUTATED                           2
  DDX41 WILD-TYPE                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX41 MUTATED                                           0     3
  DDX41 WILD-TYPE                                         1   135
D37V10, multiclass
                                           clus
vv                                          DDX41 MUTATED DDX41 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               8
  ASIAN                                                 0              19
  BLACK OR AFRICAN AMERICAN                             2              14
  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"
D37V11, binary
                 cls
clus                0   1
  DDX41 MUTATED     0   4
  DDX41 WILD-TYPE  14 130
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      0    4
  DDX41 WILD-TYPE   14  130
                        clus
vv                       DDX41 MUTATED DDX41 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             4             130
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                 cls
clus               0  1
  DDX41 MUTATED    3  1
  DDX41 WILD-TYPE 94 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      3    1
  DDX41 WILD-TYPE   94   30
            clus
vv           DDX41 MUTATED DDX41 WILD-TYPE
  TUMOR FREE             3              94
  WITH TUMOR             1              30
[1] 2 2
[1] FALSE
                 vv
clus              CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  DDX41 MUTATED        0      0       0             5       0
  DDX41 WILD-TYPE      5     10       6           154      14
D37V14, multiclass
               clus
vv              DDX41 MUTATED DDX41 WILD-TYPE
  CANADA                    0               5
  RUSSIA                    0              10
  UKRAINE                   0               6
  UNITED STATES             5             154
  VIETNAM                   0              14
[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              G1 G2 G3 G4 GX
  DDX41 MUTATED    0  2  3  0  0
  DDX41 WILD-TYPE 14 86 79  1  8
D37V15, multiclass
    clus
vv   DDX41 MUTATED DDX41 WILD-TYPE
  G1             0              14
  G2             2              86
  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"
D37V16, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1              28 
     TCGA-BI-A0VR      TCGA-C5-A1BJ      TCGA-C5-A1BL      TCGA-C5-A1BQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A2M2 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-DG-A2KK      TCGA-DS-A3LQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RA      TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3TX 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3WB      TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LB      TCGA-IR-A3LH      TCGA-JX-A3Q0      TCGA-MU-A5YI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A6DW      TCGA-Q1-A73S      TCGA-RA-A741      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V17, continuous
                 vv
clus              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DDX41 MUTATED                                             1
  DDX41 WILD-TYPE                                          25
                 vv
clus              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DDX41 MUTATED                                        0
  DDX41 WILD-TYPE                                      8
                 vv
clus              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DDX41 MUTATED                                                 0
  DDX41 WILD-TYPE                                               1
                 vv
clus              CURRENT SMOKER LIFELONG NON-SMOKER
  DDX41 MUTATED                2                   1
  DDX41 WILD-TYPE             35                  92
D37V18, multiclass
                                                 clus
vv                                                DDX41 MUTATED DDX41 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                 1              25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                      0               8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED             0               1
  CURRENT SMOKER                                              2              35
  LIFELONG NON-SMOKER                                         1              92
[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"
D37V19, continuous
D37V20, continuous
                 vv
clus              COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  DDX41 MUTATED             1        2             0        0        0
  DDX41 WILD-TYPE          19       52            12        1        7
D37V21, multiclass
               clus
vv              DDX41 MUTATED DDX41 WILD-TYPE
  COMBINATION               1              19
  EXTERNAL                  2              52
  EXTERNAL BEAM             0              12
  IMPLANTS                  0               1
  INTERNAL                  0               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"
D37V22, binary
                 cls
clus               0  1
  DDX41 MUTATED    2  0
  DDX41 WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      2    0
  DDX41 WILD-TYPE   24    3
                         clus
vv                        DDX41 MUTATED DDX41 WILD-TYPE
  COMPLETED AS PLANNED                2              24
  TREATMENT NOT COMPLETED             0               3
[1] 2 2
[1] FALSE
                 vv
clus              DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  DDX41 MUTATED                    0                0                   1
  DDX41 WILD-TYPE                  2                2                  19
                 vv
clus              REGIONAL SITE
  DDX41 MUTATED               0
  DDX41 WILD-TYPE             4
D37V23, multiclass
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1              27 
     TCGA-C5-A0TN      TCGA-C5-A1BF      TCGA-C5-A1BQ      TCGA-C5-A7CK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CM      TCGA-C5-A7CO      TCGA-C5-A7UE 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7UH      TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DS-A7WF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A43B      TCGA-EA-A5FO      TCGA-EX-A3L1      TCGA-FU-A23L 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-HM-A3JJ      TCGA-HM-A4S6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-JW-A5VG      TCGA-JX-A3Q0 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-R2-A69V      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V24, binary
                 cls
clus               0  1
  DDX41 MUTATED    0  0
  DDX41 WILD-TYPE 16  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      0    0
  DDX41 WILD-TYPE   16    4
D37V25, continuous
D37V26, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              2              99 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT      TCGA-EA-A3HU 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A449      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A770      TCGA-HG-A2PA 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC      TCGA-IR-A3LF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK      TCGA-IR-A3LL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI      TCGA-JW-A5VJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B      TCGA-JW-A852 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V27, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              2             108 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BI      TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M6      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2M2      TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CG      TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CL      TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7X3      TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EA-A5ZD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2IP      TCGA-EK-A2RK      TCGA-EX-A69L      TCGA-FU-A2QG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3YQ      TCGA-FU-A57G      TCGA-FU-A770      TCGA-HG-A2PA 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HM-A3JK      TCGA-HM-A4S6      TCGA-IR-A3L7      TCGA-IR-A3LC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V28, continuous
D37V29, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              2             107 
     TCGA-BI-A0VS      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A4BA 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A556      TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2RN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A1H6      TCGA-EX-A449      TCGA-FU-A2QG      TCGA-FU-A3EO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-IR-A3L7 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-LP-A5U2      TCGA-MU-A51Y 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V30, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              2             101 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BE      TCGA-C5-A1BI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BJ      TCGA-C5-A1BK      TCGA-C5-A1BL      TCGA-C5-A1BM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1BQ      TCGA-C5-A1M5      TCGA-C5-A1M6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT      TCGA-C5-A2LV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1      TCGA-C5-A2M2 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CH      TCGA-C5-A7CJ      TCGA-C5-A7CK      TCGA-C5-A7CL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CO      TCGA-C5-A7UE      TCGA-C5-A7UH      TCGA-C5-A7X3 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZL      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A5RQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HT      TCGA-EA-A3HU 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A44S      TCGA-EA-A556      TCGA-EA-A5O9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A2QG      TCGA-FU-A3EO      TCGA-FU-A3HY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3HZ      TCGA-FU-A3TQ      TCGA-FU-A5XV      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JK      TCGA-IR-A3L7      TCGA-IR-A3LC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH      TCGA-JW-A5VI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL      TCGA-JW-A69B 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0      TCGA-JX-A3Q8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-Q1-A73Q      TCGA-RA-A741      TCGA-UC-A7PD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-UC-A7PF 
"DDX41 WILD-TYPE" 
                 vv
clus              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DDX41 MUTATED                                     0
  DDX41 WILD-TYPE                                   2
                 vv
clus              MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  DDX41 MUTATED                                     1                       0
  DDX41 WILD-TYPE                                   6                      28
                 vv
clus              POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  DDX41 MUTATED                         0                       0
  DDX41 WILD-TYPE                       1                       6
D37V31, multiclass
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1              43 
     TCGA-BI-A20A      TCGA-C5-A0TN      TCGA-C5-A1BE      TCGA-C5-A1BK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2M1      TCGA-C5-A3HE 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ      TCGA-C5-A7UC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A50E      TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EX-A449 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-HM-A4S6      TCGA-IR-A3LH      TCGA-IR-A3LI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-UC-A7PD      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
                 vv
clus              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DDX41 MUTATED                                               0
  DDX41 WILD-TYPE                                             2
                 vv
clus              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DDX41 MUTATED                                                0
  DDX41 WILD-TYPE                                             10
                 vv
clus              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DDX41 MUTATED                                                                                   4
  DDX41 WILD-TYPE                                                                                56
                 vv
clus              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DDX41 MUTATED                                                                                              0
  DDX41 WILD-TYPE                                                                                           88
D37V32, multiclass
                                                                                              clus
vv                                                                                             DDX41 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                                                                                             DDX41 WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  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"
D37V33, binary
                 cls
clus               0  1
  DDX41 MUTATED    0  1
  DDX41 WILD-TYPE 63 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      0    1
  DDX41 WILD-TYPE   63   66
         clus
vv        DDX41 MUTATED DDX41 WILD-TYPE
  ABSENT              0              63
  PRESENT             1              66
[1] 2 2
[1] FALSE
D37V34, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1             120 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3Y4 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B      TCGA-EA-A44S 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2RA      TCGA-EK-A2RO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A3GK      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB      TCGA-IR-A3LC 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI      TCGA-IR-A3LK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8      TCGA-JX-A5QV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-MU-A5YI      TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R1 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A6DV      TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-RA-A741      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V35, continuous
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1             139 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BM      TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M9      TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MJ      TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LT      TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2M1      TCGA-C5-A3HF      TCGA-C5-A3HL      TCGA-C5-A7CG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7CJ      TCGA-C5-A7UC      TCGA-C5-A7UE      TCGA-DG-A2KH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KJ      TCGA-DG-A2KK      TCGA-DG-A2KL      TCGA-DG-A2KM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OA      TCGA-DS-A3LQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A5RQ      TCGA-DS-A7WF      TCGA-DS-A7WH      TCGA-DS-A7WI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A1QS      TCGA-EA-A1QT      TCGA-EA-A3HQ      TCGA-EA-A3HR 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HT      TCGA-EA-A3HU      TCGA-EA-A3QD      TCGA-EA-A3QE 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3Y4      TCGA-EA-A410      TCGA-EA-A411      TCGA-EA-A43B 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A44S      TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A5FO      TCGA-EA-A5O9      TCGA-EA-A6QX      TCGA-EK-A2GZ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2IP      TCGA-EK-A2PK      TCGA-EK-A2R7      TCGA-EK-A2R8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2R9      TCGA-EK-A2RA      TCGA-EK-A2RC      TCGA-EK-A2RD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RE      TCGA-EK-A2RJ      TCGA-EK-A2RK      TCGA-EK-A2RL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RM      TCGA-EK-A2RN      TCGA-EK-A2RO      TCGA-EK-A3GJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A3GK      TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A69L 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JX-A3PZ      TCGA-JX-A3Q8 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A5QV      TCGA-LP-A4AV      TCGA-LP-A4AW      TCGA-LP-A4AX 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A5U2      TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-MU-A5YI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-MY-A5BD      TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A6DV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73S      TCGA-R2-A69V      TCGA-RA-A741 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V36, binary
                 cls
clus               0  1
  DDX41 MUTATED    1  2
  DDX41 WILD-TYPE 38 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      1    2
  DDX41 WILD-TYPE   38   84
                                          clus
vv                                         DDX41 MUTATED DDX41 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                 1              38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA             2              84
[1] 2 2
[1] FALSE
D37V37, continuous
                 vv
clus              CURRENT USER FORMER USER NEVER USED
  DDX41 MUTATED              0           2          1
  DDX41 WILD-TYPE            8          41         45
D37V38, multiclass
              clus
vv             DDX41 MUTATED DDX41 WILD-TYPE
  CURRENT USER             0               8
  FORMER USER              2              41
  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"
D37V39, continuous
D37V40, binary
                 cls
clus               0  1
  DDX41 MUTATED    1  0
  DDX41 WILD-TYPE 87 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX41 MUTATED      1    0
  DDX41 WILD-TYPE   87   16
         clus
vv        DDX41 MUTATED DDX41 WILD-TYPE
  ABSENT              1              87
  PRESENT             0              16
[1] 2 2
[1] FALSE
                 vv
clus              CARBOPLATIN CISPLATIN OTHER
  DDX41 MUTATED             0         1     0
  DDX41 WILD-TYPE           2        15     1
D37V41, multiclass
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              1              18 
     TCGA-C5-A1BE      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1M9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MK      TCGA-C5-A1MN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MQ      TCGA-C5-A2LT      TCGA-C5-A2LX      TCGA-C5-A2LY 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DR-A0ZM      TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-EK-A2H0 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2H1      TCGA-HM-A3JJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V42, continuous
                 vv
clus              T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  DDX41 MUTATED      0   0    0    0  0   0    0    0   1  0   0  0  1
  DDX41 WILD-TYPE    1  21   60   22  4   7    6   10  12  1   2  2  8
D37V43, multiclass
[1] "Remove cluster labels:" "DDX41 MUTATED"         
clus
  DDX41 MUTATED DDX41 WILD-TYPE 
              2             156 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BK      TCGA-C5-A1BM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1M7      TCGA-C5-A1M8      TCGA-C5-A1M9 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1ME      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A1MP      TCGA-C5-A1MQ      TCGA-C5-A2LS      TCGA-C5-A2LT 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A2LV      TCGA-C5-A2LX      TCGA-C5-A2LY      TCGA-C5-A2M1 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A3HE      TCGA-C5-A3HL      TCGA-C5-A7CG      TCGA-C5-A7CJ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-C5-A7UC      TCGA-DG-A2KH      TCGA-DG-A2KJ      TCGA-DG-A2KK 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DG-A2KL      TCGA-DG-A2KM      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A1OA      TCGA-DS-A3LQ      TCGA-DS-A5RQ      TCGA-DS-A7WF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-DS-A7WH      TCGA-DS-A7WI      TCGA-EA-A1QS      TCGA-EA-A1QT 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3HQ      TCGA-EA-A3HR      TCGA-EA-A3HT      TCGA-EA-A3HU 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A3QD      TCGA-EA-A3QE      TCGA-EA-A3Y4      TCGA-EA-A410 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A411      TCGA-EA-A439      TCGA-EA-A43B      TCGA-EA-A44S 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A4BA      TCGA-EA-A50E      TCGA-EA-A556      TCGA-EA-A5FO 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A5O9      TCGA-EA-A5ZD      TCGA-EA-A5ZE      TCGA-EA-A5ZF 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EA-A6QX      TCGA-EA-A78R      TCGA-EK-A2IP      TCGA-EK-A2R7 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2R8      TCGA-EK-A2R9      TCGA-EK-A2RA      TCGA-EK-A2RD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RE      TCGA-EK-A2RJ      TCGA-EK-A2RK      TCGA-EK-A2RL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EK-A2RN      TCGA-EK-A3GJ      TCGA-EK-A3GK      TCGA-EK-A3GN 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A1H6      TCGA-EX-A3L1      TCGA-EX-A449      TCGA-EX-A69L 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-EX-A69M      TCGA-FU-A23K      TCGA-FU-A23L      TCGA-FU-A2QG 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3EO      TCGA-FU-A3HY      TCGA-FU-A3HZ      TCGA-FU-A3NI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A3TQ      TCGA-FU-A3TX      TCGA-FU-A3WB      TCGA-FU-A3YQ 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-FU-A40J      TCGA-FU-A57G      TCGA-FU-A5XV      TCGA-FU-A770 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HG-A2PA      TCGA-HM-A3JJ      TCGA-HM-A3JK      TCGA-HM-A4S6 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-HM-A6W2      TCGA-IR-A3L7      TCGA-IR-A3LA      TCGA-IR-A3LB 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LC      TCGA-IR-A3LF      TCGA-IR-A3LH      TCGA-IR-A3LI 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-IR-A3LK      TCGA-IR-A3LL      TCGA-JW-A5VG      TCGA-JW-A5VH 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A5VI      TCGA-JW-A5VJ      TCGA-JW-A5VK      TCGA-JW-A5VL 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JW-A69B      TCGA-JW-A852      TCGA-JX-A3PZ      TCGA-JX-A3Q0 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-JX-A3Q8      TCGA-JX-A5QV      TCGA-LP-A4AU      TCGA-LP-A4AV 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A4AW      TCGA-LP-A4AX      TCGA-LP-A5U2      TCGA-LP-A5U3 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-LP-A7HU      TCGA-MU-A51Y      TCGA-MU-A5YI      TCGA-MY-A5BD 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-MY-A5BE      TCGA-MY-A5BF      TCGA-Q1-A5R1      TCGA-Q1-A5R3 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A6DT      TCGA-Q1-A6DV      TCGA-Q1-A6DW      TCGA-Q1-A73O 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-Q1-A73P      TCGA-Q1-A73Q      TCGA-Q1-A73R      TCGA-Q1-A73S 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
     TCGA-R2-A69V      TCGA-UC-A7PD      TCGA-UC-A7PF      TCGA-WL-A834 
"DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" "DDX41 WILD-TYPE" 
D37V44, continuous
                 vv
clus              STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  DDX41 MUTATED         0        0         0         0        0         0
  DDX41 WILD-TYPE       4        1         1         1       28        53
                 vv
clus              STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  DDX41 MUTATED           0        0         0          0          0         2
  DDX41 WILD-TYPE        29        4         6          5          7        12
                 vv
clus              STAGE III STAGE IIIB STAGE IVA STAGE IVB
  DDX41 MUTATED           0          1         0         0
  DDX41 WILD-TYPE         1         28         2         5
D37V45, multiclass
            clus
vv           DDX41 MUTATED DDX41 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0               1
  STAGE IA1              0               1
  STAGE IA2              0               1
  STAGE IB               0              28
  STAGE IB1              0              53
  STAGE IB2              0              29
  STAGE II               0               4
  STAGE IIA              0               6
  STAGE IIA1             0               5
  STAGE IIA2             0               7
  STAGE IIB              2              12
  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(38) Variable = MCM7 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  MCM7 MUTATED     3   0
  MCM7 WILD-TYPE 147  40
  MCM7 MUTATED MCM7 WILD-TYPE 
             3            187 
  MCM7 MUTATED MCM7 WILD-TYPE 
             0             40 
$`MCM7 MUTATED`
TCGA-C5-A1MQ TCGA-C5-A7UE TCGA-DS-A0VL 
       33.90       155.77         2.66 

$`MCM7 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        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-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      134.33        15.48        20.35       147.35        17.19       131.11 
TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        9.34         1.12        58.88        50.76        44.94        40.04 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA 
       87.75        58.88        36.76       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 
       12.36        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        14.50        26.40        24.56        14.50        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         7.46        14.89        26.79        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       15.02        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL 
       45.96        26.27         6.64         1.51        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        47.77         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17        31.36        36.26         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         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       117.40        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-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       195.85        30.31         7.99        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        13.87        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 
       15.39        19.36        19.59         3.88        11.67        93.99 
TCGA-WL-A834 
       26.01 

  MCM7 MUTATED MCM7 WILD-TYPE 
          2.66           0.03 
  MCM7 MUTATED MCM7 WILD-TYPE 
        155.77         210.67 
  MCM7 MUTATED MCM7 WILD-TYPE 
         33.90          19.59 
[1] "2.7 - 155.8 (33.9)" "0.0 - 210.7 (19.6)"
[1] "hr="     "2.6e+07"
D38V2, continuous
                vv
clus              T1  T2 T3+T4
  MCM7 MUTATED     1   1     0
  MCM7 WILD-TYPE 103  39     5
D38V3, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2            147 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BK     TCGA-C5-A1BM     TCGA-C5-A1M5 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MP 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A3HE     TCGA-C5-A3HL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-DG-A2KH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A1QS 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR     TCGA-EA-A3HT 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE     TCGA-EA-A3Y4 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439     TCGA-EA-A43B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD     TCGA-EA-A5ZE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R     TCGA-EK-A2IP 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9     TCGA-EK-A2RA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RJ     TCGA-EK-A2RK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RL     TCGA-EK-A2RN     TCGA-EK-A3GJ     TCGA-EK-A3GK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A449 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A69L     TCGA-EX-A69M     TCGA-FU-A23K     TCGA-FU-A23L 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3HZ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3NI     TCGA-FU-A3TQ     TCGA-FU-A3TX     TCGA-FU-A3WB 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3YQ     TCGA-FU-A40J     TCGA-FU-A57G     TCGA-FU-A5XV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HG-A2PA     TCGA-HM-A3JJ     TCGA-HM-A3JK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852     TCGA-JX-A3PZ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV     TCGA-LP-A4AU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AV     TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A5U3     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DV     TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-R2-A69V 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V4, binary
                cls
clus              0  1
  MCM7 MUTATED    2  0
  MCM7 WILD-TYPE 93 44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      2    0
  MCM7 WILD-TYPE   93   44
   clus
vv  MCM7 MUTATED MCM7 WILD-TYPE
  0            2             93
  1            0             44
[1] 2 2
[1] FALSE
D38V5, binary
                cls
clus              0  1
  MCM7 MUTATED    2  0
  MCM7 WILD-TYPE 77  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      2    0
  MCM7 WILD-TYPE   77    4
   clus
vv  MCM7 MUTATED MCM7 WILD-TYPE
  0            2             77
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  MCM7 MUTATED               0                                3
  MCM7 WILD-TYPE             4                              155
                vv
clus             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  MCM7 MUTATED                                               0
  MCM7 WILD-TYPE                                             5
                vv
clus             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  MCM7 MUTATED                                     0
  MCM7 WILD-TYPE                                  22
                vv
clus             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  MCM7 MUTATED                                           0
  MCM7 WILD-TYPE                                         2
                vv
clus             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  MCM7 MUTATED                                              0
  MCM7 WILD-TYPE                                            3
D38V6, multiclass
                                               clus
vv                                              MCM7 MUTATED MCM7 WILD-TYPE
  ADENOSQUAMOUS                                            0              4
  CERVICAL SQUAMOUS CELL CARCINOMA                         3            155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE            0              5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                      0             22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                0              2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE             0              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"
D38V7, binary
                cls
clus               0   1
  MCM7 MUTATED     1   2
  MCM7 WILD-TYPE  31 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      1    2
  MCM7 WILD-TYPE   31  160
     clus
vv    MCM7 MUTATED MCM7 WILD-TYPE
  NO             1             31
  YES            2            160
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DG-A2KL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM7 MUTATED                                  0     0
  MCM7 WILD-TYPE                                8    19
                vv
clus             BLACK OR AFRICAN AMERICAN
  MCM7 MUTATED                           0
  MCM7 WILD-TYPE                        16
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCM7 MUTATED                                           0     3
  MCM7 WILD-TYPE                                         1   135
D38V10, multiclass
                                           clus
vv                                          MCM7 MUTATED MCM7 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                                                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"
D38V11, binary
                cls
clus               0   1
  MCM7 MUTATED     0   1
  MCM7 WILD-TYPE  14 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      0    1
  MCM7 WILD-TYPE   14  133
                        clus
vv                       MCM7 MUTATED MCM7 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            1            133
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                cls
clus              0  1
  MCM7 MUTATED    2  0
  MCM7 WILD-TYPE 95 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      2    0
  MCM7 WILD-TYPE   95   31
            clus
vv           MCM7 MUTATED MCM7 WILD-TYPE
  TUMOR FREE            2             95
  WITH TUMOR            0             31
[1] 2 2
[1] FALSE
                vv
clus             CANADA RUSSIA UKRAINE UNITED STATES VIETNAM
  MCM7 MUTATED        0      0       0             3       0
  MCM7 WILD-TYPE      5     10       6           156      14
D38V14, multiclass
               clus
vv              MCM7 MUTATED MCM7 WILD-TYPE
  CANADA                   0              5
  RUSSIA                   0             10
  UKRAINE                  0              6
  UNITED STATES            3            156
  VIETNAM                  0             14
[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             G1 G2 G3 G4 GX
  MCM7 MUTATED    0  3  0  0  0
  MCM7 WILD-TYPE 14 85 82  1  8
D38V15, multiclass
    clus
vv   MCM7 MUTATED MCM7 WILD-TYPE
  G1            0             14
  G2            3             85
  G3            0             82
  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"
D38V16, continuous
D38V17, continuous
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             56 
    TCGA-BI-A0VR     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A2LS     TCGA-C5-A2LT 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DG-A2KL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-EA-A556 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TQ     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A770     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A3Q0     TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
                vv
clus             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  MCM7 MUTATED                                             0
  MCM7 WILD-TYPE                                          26
                vv
clus             CURRENT REFORMED SMOKER FOR > 15 YEARS
  MCM7 MUTATED                                        0
  MCM7 WILD-TYPE                                      8
                vv
clus             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  MCM7 MUTATED                                                 0              1
  MCM7 WILD-TYPE                                               1             36
                vv
clus             LIFELONG NON-SMOKER
  MCM7 MUTATED                     2
  MCM7 WILD-TYPE                  91
D38V18, multiclass
                                                 clus
vv                                                MCM7 MUTATED MCM7 WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                0             26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                     0              8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED            0              1
  CURRENT SMOKER                                             1             36
  LIFELONG NON-SMOKER                                        2             91
[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"
D38V19, continuous
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             51 
    TCGA-BI-A0VR     TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M7     TCGA-C5-A1ME 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A2LS     TCGA-C5-A2LT 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LV     TCGA-C5-A2LX     TCGA-C5-A2LZ     TCGA-C5-A2M2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CJ     TCGA-C5-A7CL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CO     TCGA-DG-A2KK     TCGA-DR-A0ZM     TCGA-DS-A5RQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EK-A2RA     TCGA-EX-A1H5     TCGA-FU-A2QG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3EO     TCGA-FU-A3HY     TCGA-FU-A3TQ     TCGA-FU-A3TX 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A5XV     TCGA-FU-A770 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LB 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-JW-A5VI     TCGA-JW-A5VK     TCGA-JX-A3Q0 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-Q1-A6DW     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V20, continuous
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2             80 
    TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1M6     TCGA-C5-A1M8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ML     TCGA-C5-A2LT     TCGA-C5-A2LX     TCGA-C5-A2LY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LZ     TCGA-C5-A3HD     TCGA-C5-A3HF     TCGA-C5-A7CL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CM     TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DG-A2KM     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WH     TCGA-DS-A7WI     TCGA-EA-A3QD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EK-A2H0     TCGA-EX-A3L1 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A449     TCGA-FU-A23L     TCGA-FU-A3HY     TCGA-FU-A3HZ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AX     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A5R3     TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73Q 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
                vv
clus             COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  MCM7 MUTATED             1        1             0        0        0
  MCM7 WILD-TYPE          19       53            12        1        7
D38V21, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2             92 
    TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BJ     TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BQ     TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN     TCGA-C5-A2LT 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A3HD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HE     TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO     TCGA-C5-A7UH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A3QD     TCGA-EA-A3Y4     TCGA-EA-A43B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A5FO     TCGA-EA-A5O9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2H0     TCGA-EX-A3L1     TCGA-EX-A449     TCGA-FU-A23L 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A3JK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7     TCGA-IR-A3LA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF     TCGA-IR-A3LH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL     TCGA-JW-A5VG 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JX-A3Q0     TCGA-JX-A5QV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AU     TCGA-LP-A4AX     TCGA-LP-A7HU     TCGA-MU-A5YI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BF     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73Q     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-RA-A741     TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V22, binary
                cls
clus              0  1
  MCM7 MUTATED    1  0
  MCM7 WILD-TYPE 25  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      1    0
  MCM7 WILD-TYPE   25    3
                         clus
vv                        MCM7 MUTATED MCM7 WILD-TYPE
  COMPLETED AS PLANNED               1             25
  TREATMENT NOT COMPLETED            0              3
[1] 2 2
[1] FALSE
                vv
clus             DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  MCM7 MUTATED                    0                0                   1
  MCM7 WILD-TYPE                  2                2                  19
                vv
clus             REGIONAL SITE
  MCM7 MUTATED               0
  MCM7 WILD-TYPE             4
D38V23, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             27 
    TCGA-C5-A0TN     TCGA-C5-A1BF     TCGA-C5-A1BQ     TCGA-C5-A2LZ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CK     TCGA-C5-A7CL     TCGA-C5-A7CM     TCGA-C5-A7CO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7UH     TCGA-C5-A7X3     TCGA-DG-A2KL     TCGA-DS-A7WF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A5FO     TCGA-EX-A3L1     TCGA-FU-A23L 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-HM-A3JJ     TCGA-HM-A4S6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-JW-A5VG     TCGA-JX-A3Q0 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-R2-A69V     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V24, binary
                cls
clus              0  1
  MCM7 MUTATED    0  0
  MCM7 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      0    0
  MCM7 WILD-TYPE   16    4
D38V25, continuous
D38V26, continuous
D38V27, continuous
D38V28, continuous
D38V29, continuous
D38V30, continuous
                vv
clus             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  MCM7 MUTATED                                     0
  MCM7 WILD-TYPE                                   2
                vv
clus             MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  MCM7 MUTATED                                     1                       1
  MCM7 WILD-TYPE                                   6                      27
                vv
clus             POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  MCM7 MUTATED                         0                       0
  MCM7 WILD-TYPE                       1                       6
D38V31, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2             42 
    TCGA-BI-A20A     TCGA-C5-A0TN     TCGA-C5-A1BE     TCGA-C5-A1BK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2M1     TCGA-C5-A3HE     TCGA-C5-A3HL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC     TCGA-DG-A2KL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EA-A50E     TCGA-EK-A2RN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-EX-A1H5     TCGA-EX-A449     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A4S6     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
                vv
clus             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  MCM7 MUTATED                                               0
  MCM7 WILD-TYPE                                             2
                vv
clus             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  MCM7 MUTATED                                                0
  MCM7 WILD-TYPE                                             10
                vv
clus             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  MCM7 MUTATED                                                                                   0
  MCM7 WILD-TYPE                                                                                60
                vv
clus             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  MCM7 MUTATED                                                                                              1
  MCM7 WILD-TYPE                                                                                           87
D38V32, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1            159 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A0TN     TCGA-C5-A1BE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK     TCGA-C5-A1BL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BM     TCGA-C5-A1BN     TCGA-C5-A1BQ     TCGA-C5-A1M5 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-C5-A2LT     TCGA-C5-A2LV     TCGA-C5-A2LX 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LY     TCGA-C5-A2LZ     TCGA-C5-A2M1     TCGA-C5-A2M2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HF     TCGA-C5-A3HL     TCGA-C5-A7CO     TCGA-DG-A2KH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KK     TCGA-DG-A2KL     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A7WI     TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HR     TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3QE     TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A439     TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZD     TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A78R     TCGA-EK-A2GZ     TCGA-EK-A2H0     TCGA-EK-A2H1 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2PG     TCGA-EK-A2PM     TCGA-EK-A2R7     TCGA-EK-A2R8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RK     TCGA-EK-A2RN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RO     TCGA-EK-A3GM     TCGA-EX-A1H5     TCGA-EX-A1H6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A3YQ     TCGA-FU-A40J     TCGA-FU-A57G 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA     TCGA-HM-A3JJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2     TCGA-IR-A3L7 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC     TCGA-IR-A3LF 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK     TCGA-IR-A3LL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI     TCGA-JW-A5VJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B     TCGA-JW-A852 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8     TCGA-JX-A5QV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AU     TCGA-LP-A4AW     TCGA-LP-A4AX     TCGA-LP-A5U2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A5U3     TCGA-LP-A7HU     TCGA-MU-A51Y     TCGA-MU-A5YI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BD     TCGA-MY-A5BE     TCGA-MY-A5BF     TCGA-Q1-A5R1 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DT     TCGA-Q1-A6DV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DW     TCGA-Q1-A73O     TCGA-Q1-A73P     TCGA-Q1-A73Q 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73R     TCGA-Q1-A73S     TCGA-R2-A69V     TCGA-RA-A741 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V33, binary
                cls
clus              0  1
  MCM7 MUTATED    0  2
  MCM7 WILD-TYPE 63 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      0    2
  MCM7 WILD-TYPE   63   65
         clus
vv        MCM7 MUTATED MCM7 WILD-TYPE
  ABSENT             0             63
  PRESENT            2             65
[1] 2 2
[1] FALSE
D38V34, continuous
D38V35, continuous
D38V36, binary
                cls
clus              0  1
  MCM7 MUTATED    0  1
  MCM7 WILD-TYPE 39 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      0    1
  MCM7 WILD-TYPE   39   85
                                          clus
vv                                         MCM7 MUTATED MCM7 WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                0             39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA            1             85
[1] 2 2
[1] FALSE
D38V37, continuous
                vv
clus             CURRENT USER FORMER USER NEVER USED
  MCM7 MUTATED              0           0          1
  MCM7 WILD-TYPE            8          43         45
D38V38, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             96 
    TCGA-C5-A1BI     TCGA-C5-A1BL     TCGA-C5-A1BN     TCGA-C5-A1M6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9     TCGA-C5-A1ME 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MN     TCGA-C5-A2LT     TCGA-C5-A2LV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A2M2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HD     TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7UH 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A7X3     TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A3LQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A43B     TCGA-EA-A44S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A4BA     TCGA-EA-A50E     TCGA-EA-A556     TCGA-EA-A5O9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EK-A2R7     TCGA-EK-A3GK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-EX-A1H6     TCGA-EX-A3L1     TCGA-EX-A69L 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A69M     TCGA-FU-A2QG     TCGA-FU-A3EO     TCGA-FU-A3HY 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A57G     TCGA-FU-A770 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VG     TCGA-JW-A5VI     TCGA-JW-A5VJ     TCGA-JW-A5VK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A69B     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3     TCGA-Q1-A6DV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73S     TCGA-UC-A7PD     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V39, continuous
D38V40, binary
                cls
clus              0  1
  MCM7 MUTATED    2  0
  MCM7 WILD-TYPE 86 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM7 MUTATED      2    0
  MCM7 WILD-TYPE   86   16
         clus
vv        MCM7 MUTATED MCM7 WILD-TYPE
  ABSENT             2             86
  PRESENT            0             16
[1] 2 2
[1] FALSE
                vv
clus             CARBOPLATIN CISPLATIN OTHER
  MCM7 MUTATED             0         1     0
  MCM7 WILD-TYPE           2        15     1
D38V41, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             1             18 
    TCGA-C5-A1BE     TCGA-C5-A1BI     TCGA-C5-A1BN     TCGA-C5-A1M9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MH     TCGA-C5-A1MI     TCGA-C5-A1MK     TCGA-C5-A1MN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LT     TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A3HD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-DS-A1OA     TCGA-DS-A3LQ     TCGA-EK-A2H0 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2H1     TCGA-HM-A3JJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V42, continuous
                vv
clus             T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TX
  MCM7 MUTATED      0   0    1    0  0   0    0    0   1  0   0  0  0
  MCM7 WILD-TYPE    1  21   59   22  4   7    6   10  12  1   2  2  9
D38V43, multiclass
[1] "Remove cluster labels:" "MCM7 MUTATED"          
clus
  MCM7 MUTATED MCM7 WILD-TYPE 
             2            156 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BK     TCGA-C5-A1BM 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-C5-A2LS     TCGA-C5-A2LT     TCGA-C5-A2LV 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A2LX     TCGA-C5-A2LY     TCGA-C5-A2M1     TCGA-C5-A3HE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-C5-A3HL     TCGA-C5-A7CG     TCGA-C5-A7CJ     TCGA-C5-A7UC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KH     TCGA-DG-A2KJ     TCGA-DG-A2KK     TCGA-DG-A2KL 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DG-A2KM     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OA     TCGA-DS-A3LQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-DS-A5RQ     TCGA-DS-A7WF     TCGA-DS-A7WH     TCGA-DS-A7WI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A1QS     TCGA-EA-A1QT     TCGA-EA-A3HQ     TCGA-EA-A3HR 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3HT     TCGA-EA-A3HU     TCGA-EA-A3QD     TCGA-EA-A3QE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A3Y4     TCGA-EA-A410     TCGA-EA-A411     TCGA-EA-A439 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A43B     TCGA-EA-A44S     TCGA-EA-A4BA     TCGA-EA-A50E 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A556     TCGA-EA-A5FO     TCGA-EA-A5O9     TCGA-EA-A5ZD 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EA-A5ZE     TCGA-EA-A5ZF     TCGA-EA-A6QX     TCGA-EA-A78R 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2IP     TCGA-EK-A2R7     TCGA-EK-A2R8     TCGA-EK-A2R9 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RA     TCGA-EK-A2RD     TCGA-EK-A2RE     TCGA-EK-A2RJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A2RK     TCGA-EK-A2RL     TCGA-EK-A2RN     TCGA-EK-A3GJ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EK-A3GK     TCGA-EK-A3GN     TCGA-EX-A1H5     TCGA-EX-A1H6 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-EX-A3L1     TCGA-EX-A449     TCGA-EX-A69L     TCGA-EX-A69M 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L     TCGA-FU-A2QG     TCGA-FU-A3EO 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3HY     TCGA-FU-A3HZ     TCGA-FU-A3NI     TCGA-FU-A3TQ 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A3TX     TCGA-FU-A3WB     TCGA-FU-A3YQ     TCGA-FU-A40J 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-FU-A57G     TCGA-FU-A5XV     TCGA-FU-A770     TCGA-HG-A2PA 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-HM-A3JJ     TCGA-HM-A3JK     TCGA-HM-A4S6     TCGA-HM-A6W2 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3L7     TCGA-IR-A3LA     TCGA-IR-A3LB     TCGA-IR-A3LC 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LF     TCGA-IR-A3LH     TCGA-IR-A3LI     TCGA-IR-A3LK 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-IR-A3LL     TCGA-JW-A5VG     TCGA-JW-A5VH     TCGA-JW-A5VI 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A5VJ     TCGA-JW-A5VK     TCGA-JW-A5VL     TCGA-JW-A69B 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JW-A852     TCGA-JX-A3PZ     TCGA-JX-A3Q0     TCGA-JX-A3Q8 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-JX-A5QV     TCGA-LP-A4AU     TCGA-LP-A4AV     TCGA-LP-A4AW 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-LP-A4AX     TCGA-LP-A5U2     TCGA-LP-A5U3     TCGA-LP-A7HU 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MU-A51Y     TCGA-MU-A5YI     TCGA-MY-A5BD     TCGA-MY-A5BE 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-MY-A5BF     TCGA-Q1-A5R1     TCGA-Q1-A5R2     TCGA-Q1-A5R3 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A6DT     TCGA-Q1-A6DV     TCGA-Q1-A6DW     TCGA-Q1-A73O 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-Q1-A73P     TCGA-Q1-A73Q     TCGA-Q1-A73R     TCGA-Q1-A73S 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
    TCGA-R2-A69V     TCGA-UC-A7PD     TCGA-UC-A7PF     TCGA-WL-A834 
"MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" "MCM7 WILD-TYPE" 
D38V44, continuous
                vv
clus             STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  MCM7 MUTATED         0        0         0         0        1         1
  MCM7 WILD-TYPE       4        1         1         1       27        52
                vv
clus             STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB
  MCM7 MUTATED           0        0         1          0          0         0
  MCM7 WILD-TYPE        29        4         5          5          7        14
                vv
clus             STAGE III STAGE IIIB STAGE IVA STAGE IVB
  MCM7 MUTATED           0          0         0         0
  MCM7 WILD-TYPE         1         29         2         5
D38V45, multiclass
            clus
vv           MCM7 MUTATED MCM7 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             1              5
  STAGE IIA1            0              5
  STAGE IIA2            0              7
  STAGE IIB             0             14
  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"
