[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTCESC-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/10005797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/10668125/CESC-TP.mergedcluster.txt"

nPatients in clinical file=200, in cluster file=256, common to both=200
[1]   8 200
[1] "CN_CNMF"
[1] 3
 1  2  3 
55 39 82 
 1  2  3 
55 39 82 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6 
45 32 38 42 31 12 
 1  2  3  4  5  6 
45 32 38 42 31 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
77 47 56 
 1  2  3 
77 47 56 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
91 25 17 47 
 1  2  3  4 
91 25 17 47 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
62 60 78 
 1  2  3 
62 60 78 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 37 123  40 
  1   2   3 
 37 123  40 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
64 65 71 
 1  2  3 
64 65 71 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
23 40 17 31 29 27 33 
 1  2  3  4  5  6  7 
23 40 17 31 29 27 33 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDESEASE"                            
 [6] "NEOPLASM.DISEASESTAGE"                           
 [7] "PATHOLOGY.T.STAGE"                               
 [8] "PATHOLOGY.N.STAGE"                               
 [9] "PATHOLOGY.M.STAGE"                               
[10] "DCCUPLOADDATE"                                   
[11] "GENDER"                                          
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                
[13] "HISTOLOGICALTYPE"                                
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"          
[15] "NUMBERPACKYEARSSMOKED"                           
[16] "NUMBER.OF.LYMPH.NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCHNUMBER"                                     
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASMHISTOLOGICGRADE"                         
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_THERAPY_TYPE"                          
[30] "RADIATION_THERAPY_STATUS"                        
[31] "RADIATION_ADJUVANT_UNITS"                        
[32] "PREGNANCIES_COUNT_TOTAL"                         
[33] "PREGNANCIES_COUNT_STILLBIRTH"                    
[34] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[35] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_ECTOPIC"                       
[38] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[39] "LYMPH_NODE_LOCATION"                             
[40] "LOCATION_OF_POSITIVE_MARGINS"                    
[41] "MENOPAUSE_STATUS"                                
[42] "LYMPHOVASCULAR_INVOLVEMENT"                      
[43] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[44] "LYMPH_NODES_EXAMINED"                            
[45] "KERATINIZATION_SQUAMOUS_CELL"                    
[46] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[47] "HYSTERECTOMY_TYPE"                               
[48] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[49] "HEIGHT_CM_AT_DIAGNOSIS"                          
[50] "FEDPET_OR_CT_RESULTS"                            
[51] "CORPUS_INVOLVEMENT"                              
[52] "CHEMO_CONCURRENT_TYPE"                           
[53] "CERVIX_SUV_RESULTS"                              
[54] "CAUSE_OF_DEATH"                                  
[55] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[56] "AGE_AT_DIAGNOSIS"                                

Input Data has 56 rows and 200 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
        1505         1735          720           NA           NA           NA 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
        1112         4385         5385         5271           NA           NA 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
          NA           NA           NA         1409          919           NA 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
        1756         1617           NA           NA           NA           NA 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
          NA          109         1031         1345         2226         2234 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
        2526         2383           NA         1169           25         1582 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
         548           NA          621         5564          771           NA 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
          NA           NA          294         2233           NA         2602 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
        1846           NA           NA           NA           83         1551 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
          NA          254         2305         3039           NA           NA 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 
         186          636          518          149         4879          136 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
        2669         1791           NA           81         3589         3609 
TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ 
         266          879           NA          376         3874          699 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
         512           NA          223           NA           23          376 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
          53           40           25           19           81          397 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
          36          441           41           41          441           55 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
         385          390            8          453           45          423 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
          21          456          455          413          410           11 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PI 
         383         1398          202         2679           16           NA 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
          NA           NA           NA           18            2          123 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM 
           1           11           36           NA          721           68 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
           3            2            3            3           NA            1 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
         619          241          211          447          136          186 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
         144           37          725           28           66           20 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
          31           44           48           45           25          107 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
          41           40           60           34          773           NA 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
         632          454          125         4483         4172           NA 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
        3571         2949         2394         2493          808         1106 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
         439          506          588          623          474          306 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
         156            3           NA           27            2           25 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
         422            1          165          904            2          132 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
         167           90          113          105          178          103 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
         113          175          146          190          596          118 
TCGA-UC-A7PD TCGA-UC-A7PF 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=137,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=14,	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:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
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:'NUMBERPACKYEARSSMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=11,	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=18,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=64,	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:'NEOPLASMHISTOLOGICGRADE':	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=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 31:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 33:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 39:'LYMPH_NODE_LOCATION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 40:'LOCATION_OF_POSITIVE_MARGINS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 41:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'HYSTERECTOMY_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 49:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 50:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 51:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 52:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 53:'CERVIX_SUV_RESULTS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 55:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 56:'AGE_AT_DIAGNOSIS':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                             
 [2] "PATHOLOGY.T.STAGE"                               
 [3] "PATHOLOGY.N.STAGE"                               
 [4] "PATHOLOGY.M.STAGE"                               
 [5] "HISTOLOGICAL.TYPE"                               
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"          
 [7] "NUMBERPACKYEARSSMOKED"                           
 [8] "NUMBER.OF.LYMPH.NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASMHISTOLOGICGRADE"                         
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_THERAPY_TYPE"                          
[20] "RADIATION_ADJUVANT_UNITS"                        
[21] "PREGNANCIES_COUNT_TOTAL"                         
[22] "PREGNANCIES_COUNT_STILLBIRTH"                    
[23] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[24] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[25] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[26] "PREGNANCIES_COUNT_ECTOPIC"                       
[27] "LYMPH_NODE_LOCATION"                             
[28] "LOCATION_OF_POSITIVE_MARGINS"                    
[29] "MENOPAUSE_STATUS"                                
[30] "LYMPHOVASCULAR_INVOLVEMENT"                      
[31] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[32] "LYMPH_NODES_EXAMINED"                            
[33] "KERATINIZATION_SQUAMOUS_CELL"                    
[34] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[35] "HYSTERECTOMY_TYPE"                               
[36] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[37] "HEIGHT_CM_AT_DIAGNOSIS"                          
[38] "CORPUS_INVOLVEMENT"                              
[39] "CHEMO_CONCURRENT_TYPE"                           
[40] "CERVIX_SUV_RESULTS"                              
[41] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[42] "AGE_AT_DIAGNOSIS"                                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 200 columns, 1 survival variables, and 42 non-survival variables.
AGE, 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 
108  39   2   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  108    39     4 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
108  39   2   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  108    39     4 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=28, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=11, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=64, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASMHISTOLOGICGRADE, 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=20, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, 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=11, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
LYMPH_NODE_LOCATION, nv=4, binary=FALSE, numeric=FALSE
LOCATION_OF_POSITIVE_MARGINS, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=11, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=47, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=19, binary=FALSE, numeric=TRUE
HYSTERECTOMY_TYPE, nv=3, binary=FALSE, numeric=FALSE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=33, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=2, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=10, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=14, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=58, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 45  8
  subtype2 26  9
  subtype3 66 15
subtype1 subtype2 subtype3 
      53       35       81 
subtype1 subtype2 subtype3 
       8        9       15 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M6 
       49.48        57.04        68.84       173.29        67.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 
       30.21        53.16        44.22        83.05       100.14         0.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A0VL 
      134.33        85.55        13.61         2.73        36.76         2.66 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       22.98        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50        14.89        13.91         0.69        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GN 
       13.48        12.59         0.03        23.70         0.07         0.03 
TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A4S6 TCGA-IR-A3LC 
       20.35         6.12        23.84         1.45        14.93       117.40 
TCGA-IR-A3LI TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MY-A5BD 
       81.96        20.48         5.13         0.89         0.82        29.72 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-UC-A7PF 
        3.72         3.45         5.85         5.75        93.99 

$subtype2
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LT 
       23.67        11.44         5.46        35.61        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7CM 
       73.45        78.35        52.01        25.35        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A7WI TCGA-EA-A3QD 
       73.41        60.69        87.75       117.99         8.28        13.05 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ 
        1.35         1.81        45.96         0.53         0.59         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-FU-A40J TCGA-FU-A5XV TCGA-HM-A3JJ 
        2.24         0.10         0.10         1.35         1.97        21.67 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-UC-A7PD 
       78.71        26.56         2.96         3.39        11.67 

$subtype3
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ 
       18.74        36.56       144.16       177.04        82.85        19.86 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       46.32        35.01        57.73        38.99         0.46         2.43 
TCGA-C5-A1MP TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        3.58        38.43        18.02        17.85        20.42       182.93 
TCGA-C5-A7CJ TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZM TCGA-DS-A0VN 
      101.82        17.19        94.95         9.34        58.88       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3QE TCGA-EA-A3Y4 
       16.83        16.18         7.33         0.76         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A6QX 
        1.35        12.66        12.82         0.26         1.48        13.58 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EX-A1H6 
        6.64         0.07         4.04         0.36         0.10         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        6.94        14.70         4.47         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.32         1.12        25.41        20.78         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
      137.16        66.81        96.95        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A51Y 
       19.33        15.58        10.06         0.10         0.07        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73P 
        0.03         5.42         0.07         4.34         3.72         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        6.25        19.59         3.88 

subtype1 subtype2 subtype3 
    0.03     0.10     0.03 
subtype1 subtype2 subtype3 
  173.29   117.99   182.93 
subtype1 subtype2 subtype3 
   14.89    13.05    10.06 
[1] "0.0 - 173.3 (14.9)" "0.1 - 118.0 (13.1)" "0.0 - 182.9 (10.1)"
D1V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 30 11     1
  subtype2 19  5     0
  subtype3 48 20     2
D1V3, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          30       19       48
  T2          11        5       20
  T3+T4        1        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
          cls
clus        0  1
  subtype1 25 14
  subtype2 13 11
  subtype3 49 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   14
  subtype2   13   11
  subtype3   49   15
   clus
vv  subtype1 subtype2 subtype3
  0       25       13       49
  1       14       11       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 28  1 16
  subtype2 14  0 11
  subtype3 30  2 38
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       28       14       30
  M1        1        0        2
  MX       16       11       38
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             0                               48
  subtype2             0                               35
  subtype3             2                               61
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             1
  subtype2                                             1
  subtype3                                             2
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   3
  subtype2                                   3
  subtype3                                  14
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         1
  subtype2                                         0
  subtype3                                         1
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            2
  subtype2                                            0
  subtype3                                            2
D1V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        0        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    48       35       61
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1        1        2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  3        3       14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            1        0        1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         2        0        2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  8 47
  subtype2  7 32
  subtype3 12 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   47
  subtype2    7   32
  subtype3   12   70
     clus
vv    subtype1 subtype2 subtype3
  NO         8        7       12
  YES       47       32       70
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                         5
  subtype2                                1     1                         6
  subtype3                                4     6                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    38
  subtype2                                         0    31
  subtype3                                         1    61
D1V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 2        1        4
  ASIAN                                            8        1        6
  BLACK OR AFRICAN AMERICAN                        5        6        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           38       31       61
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
          cls
clus        0  1
  subtype1  3 40
  subtype2  2 29
  subtype3  6 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   40
  subtype2    2   29
  subtype3    6   58
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        6
  NOT HISPANIC OR LATINO       40       29       58
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
D1V13, binary
          cls
clus        0  1
  subtype1 17  5
  subtype2 10  6
  subtype3 21  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    5
  subtype2   10    6
  subtype3   21    8
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       17       10       21
  WITH TUMOR        5        6        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       0      6       1            40       8
  subtype2       1      1       1            36       0
  subtype3       0      3       4            71       4
D1V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  NIGERIA              0        1        0
  RUSSIA               6        1        3
  UKRAINE              1        1        4
  UNITED STATES       40       36       71
  VIETNAM              8        0        4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 30 18  0  1
  subtype2  0 14 23  1  1
  subtype3  8 39 31  0  3
D1V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        0        8
  G2       30       14       39
  G3       18       23       31
  G4        0        1        0
  GX        1        1        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V16, continuous
D1V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  subtype2                                           3
  subtype3                                          11
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      4
  subtype2                                      1
  subtype3                                      3
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             10
  subtype2                                               0              8
  subtype3                                               0             18
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  26
  subtype2                  14
  subtype3                  43
D1V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        3       11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 4        1        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0        0
  CURRENT SMOKER                                        10        8       18
  LIFELONG NON-SMOKER                                   26       14       43
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           6       12             3        0
  subtype2           4        6             3        4
  subtype3           7       19             5        1
D1V20, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          6        4        7
  EXTERNAL            12        6       19
  EXTERNAL BEAM        3        3        5
  INTERNAL             0        4        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V21, binary
          cls
clus       0 1
  subtype1 2 0
  subtype2 5 1
  subtype3 4 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    0
  subtype2    5    1
  subtype3    4    2
     clus
vv    subtype1 subtype2 subtype3
  CGY        2        5        4
  GY         0        1        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
D1V26, continuous
D1V27, continuous
          vv
clus       2003 COMMON ILIAC PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1    0            0                                                 15
  subtype2    1            0                                                  7
  subtype3    0            1                                                 16
D1V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        1        0
  COMMON ILIAC                                              0        0        1
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)       15        7       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       4
  subtype2                                   3                       3
  subtype3                                   1                       2
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       0                       1
  subtype3                       1                       2
D1V29, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        3        1
  OTHER LOCATION, SPECIFY                    4        3        2
  POSITIVE BLADDER MARGIN                    0        0        1
  POSITIVE VAGINAL MARGIN                    2        1        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             2
  subtype2                                             0
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              5
  subtype2                                              1
  subtype3                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                19
  subtype2                                                                                12
  subtype3                                                                                23
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           20
  subtype2                                                                                           16
  subtype3                                                                                           41
D1V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       20
                                                                                              clus
vv                                                                                             subtype2
  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)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       41
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V31, binary
          cls
clus        0  1
  subtype1 18 19
  subtype2  8 16
  subtype3 28 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   19
  subtype2    8   16
  subtype3   28   24
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        18        8       28
  PRESENT       19       16       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V32, continuous
D1V33, continuous
D1V34, binary
          cls
clus        0  1
  subtype1 12 26
  subtype2  9 16
  subtype3 14 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   26
  subtype2    9   16
  subtype3   14   39
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           12        9       14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       26       16       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     0                   37                   0
  subtype2     0                   24                   0
  subtype3     3                   52                   5
D1V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3
  OTHER                       0        0        3
  RADICAL HYSTERECTOMY       37       24       52
  SIMPLE HYSTERECTOMY         0        0        5
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            2          10         16
  subtype2            3          11          6
  subtype3            3          19         18
D1V37, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        2        3        3
  FORMER USER        10       11       19
  NEVER USED         16        6       18
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V38, continuous
D1V39, binary
          cls
clus        0  1
  subtype1 26  7
  subtype2 13  1
  subtype3 34  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    7
  subtype2   13    1
  subtype3   34    6
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        26       13       34
  PRESENT        7        1        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V40, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 0 7
  subtype3 1 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    0    7
  subtype3    1    4
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        0        1
  CISPLATIN          3        7        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V41, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        2        5 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  subtype1   2    0   8   14    6  1   3    2    0   5   1  0  4
  subtype2   0    0   4   12    3  0   0    2    1   2   0  0  1
  subtype3   0    1  10   25   12  2   3    2    7   6   1  1  2
D1V42, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         2        0        0
  T1A1        0        0        1
  T1B         8        4       10
  T1B1       14       12       25
  T1B2        6        3       12
  T2          1        0        2
  T2A         3        0        3
  T2A1        2        2        2
  T2A2        0        1        7
  T2B         5        2        6
  T3B         1        0        1
  T4          0        0        1
  TX          4        1        2
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V43, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 37  7
  subtype2 28  4
  subtype3 29  9
  subtype4 26 13
  subtype5 24  4
  subtype6 11  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      44       32       38       39       28       12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7        4        9       13        4        1 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS 
       31.40        35.01        57.73        35.61         0.46        44.22 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 
       38.43         0.82        18.02        17.85         9.67         2.73 
TCGA-C5-A8YT TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA 
        6.12        16.18         7.33         1.35        14.50        12.82 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK 
       14.89        14.96         0.59        23.70         2.24         0.10 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
        7.92        14.70         4.73         1.22         2.17         1.02 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.35         1.32         1.12         4.11       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A69B TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 
       96.95        81.96        10.06        29.72         2.96         3.72 
TCGA-Q1-A6DV TCGA-Q1-A73P 
        3.72         4.80 

$subtype2
TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A7CO TCGA-C5-A7UH 
      173.29        67.46        83.05       100.14        73.41        60.69 
TCGA-C5-A901 TCGA-C5-A905 TCGA-DS-A0VM TCGA-DS-A1OA TCGA-EA-A1QT TCGA-EA-A3HQ 
       17.03       160.41       117.99        28.90        12.36         1.74 
TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB 
       12.66         1.48        13.58         6.64         0.53         0.07 
TCGA-EK-A2RC TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-IR-A3L7 
        4.04         0.92         0.66         1.58         1.97       147.39 
TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A5U3 
      117.40        26.56        20.48        15.58         5.13         0.82 
TCGA-Q1-A5R2 TCGA-Q1-A73R 
        3.45         6.25 

$subtype3
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ 
       49.48        36.56       144.16       177.04        82.85        19.86 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A7CG TCGA-C5-A7CJ 
       46.32        38.99         2.43         3.58       182.93       101.82 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A1O9 
       94.95         9.34        50.99        87.75        58.88         8.75 
TCGA-DS-A1OD TCGA-EA-A1QS TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A5ZD 
      127.36         0.76         2.66        13.05         1.18         0.69 
TCGA-EA-A78R TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3YQ 
       13.48         0.03         0.10         6.94         4.47         3.52 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y 
       21.67        14.93        36.36         0.10         0.89        13.87 
TCGA-MY-A5BE TCGA-R2-A69V 
        0.07        19.59 

$subtype4
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A1MQ 
       57.04        11.44        18.74         5.46        40.93        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL 
       73.18        73.45        78.35        52.01        25.35        15.48 
TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       17.19        13.61        45.83        99.91        23.51        27.52 
TCGA-C5-A907 TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B 
        4.47       118.65        12.36         8.28        14.50         1.81 
TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EK-A2H0 TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ 
        0.26        13.91        45.96         0.36         1.18         0.10 
TCGA-EK-A3GN TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-LP-A4AX 
        0.03        78.71        14.43        16.64        19.33         0.07 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-UC-A7PD 
        5.49         3.39        11.67 

$subtype5
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1M8 TCGA-C5-A3HL TCGA-C5-A7CK TCGA-C5-A7UE 
       23.67        68.84        30.21        20.42       134.33        85.55 
TCGA-C5-A8XJ TCGA-C5-A8ZZ TCGA-DS-A0VK TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-DS-A5RQ 
       75.78        20.91        36.76        28.31        22.98        16.83 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A97N TCGA-EK-A2IR 
        1.32         0.82         0.62         1.35         0.36        88.08 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3TX TCGA-FU-A3WB TCGA-HG-A2PA 
        0.07        20.35        23.84         1.48         0.82        25.41 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-Q1-A6DW TCGA-UC-A7PF 
        0.03         5.42         5.75        93.99 

$subtype6
TCGA-C5-A1MF TCGA-C5-A8XI TCGA-C5-A902 TCGA-DS-A0VL TCGA-EA-A5ZE TCGA-EK-A2GZ 
       53.16         8.35         4.90         2.66        14.99        12.59 
TCGA-EX-A69M TCGA-FU-A3NI TCGA-HM-A3JK TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-RA-A741 
        6.12         1.45        20.78         4.34         5.85         3.88 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.07     0.03     0.03     0.03     1.45 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  137.16   173.29   182.93   118.65   134.33    53.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   8.795   13.120   14.400   15.480   20.665    5.985 
[1] "0.1 - 137.2 (8.8)"  "0.1 - 173.3 (13.1)" "0.0 - 182.9 (14.4)"
[4] "0.0 - 118.7 (15.5)" "0.0 - 134.3 (20.7)" "1.4 - 53.2 (6.0)"  
D2V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 25 12     1
  subtype2 18  5     0
  subtype3 23  9     1
  subtype4 18  7     1
  subtype5 18  4     1
  subtype6  6  2     0
D2V3, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1          25       18       23       18       18        6
  T2          12        5        9        7        4        2
  T3+T4        1        0        1        1        1        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus        0  1
  subtype1 26  9
  subtype2 11 11
  subtype3 21 11
  subtype4 20  5
  subtype5 16  6
  subtype6  6  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    9
  subtype2   11   11
  subtype3   21   11
  subtype4   20    5
  subtype5   16    6
  subtype6    6    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       26       11       21       20       16        6
  1        9       11       11        5        6        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 20  3 15
  subtype2 13  0 12
  subtype3 19  0 14
  subtype4 16  1 11
  subtype5 12  0 12
  subtype6  3  0  6
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       20       13       19       16       12        3
  M1        3        0        0        1        0        0
  MX       15       12       14       11       12        6
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               14
  subtype2             0                               31
  subtype3             0                               38
  subtype4             0                               42
  subtype5             0                               31
  subtype6             0                               12
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
  subtype6                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
  subtype6                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            4
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
  subtype5                                            0
  subtype6                                            0
D2V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    14       31       38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         4        0        0
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    42       31       12
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0        0
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  4 41
  subtype2  3 29
  subtype3  8 30
  subtype4  9 33
  subtype5  6 25
  subtype6  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   41
  subtype2    3   29
  subtype3    8   30
  subtype4    9   33
  subtype5    6   25
  subtype6    2   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         4        3        8        9        6        2
  YES       41       29       30       33       25       10
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         3
  subtype2                                1     3                         3
  subtype3                                1     6                         6
  subtype4                                4     3                         6
  subtype5                                1     0                         2
  subtype6                                0     1                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    38
  subtype2                                         0    24
  subtype3                                         0    25
  subtype4                                         1    28
  subtype5                                         0    25
  subtype6                                         0     8
D2V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        1        4
  ASIAN                                            3        3        6        3
  BLACK OR AFRICAN AMERICAN                        3        3        6        6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           38       24       25       28
                                           clus
vv                                          subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0
  ASIAN                                            0        1
  BLACK OR AFRICAN AMERICAN                        2        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0
  WHITE                                           25        8
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
          cls
clus        0  1
  subtype1  5 32
  subtype2  2 22
  subtype3  0 33
  subtype4  5 28
  subtype5  1 20
  subtype6  0  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   32
  subtype2    2   22
  subtype3    0   33
  subtype4    5   28
  subtype5    1   20
  subtype6    0    9
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            5        2        0        5        1        0
  NOT HISPANIC OR LATINO       32       22       33       28       20        9
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
D2V13, binary
          cls
clus        0  1
  subtype1  9  6
  subtype2  8  4
  subtype3 12  4
  subtype4 12  6
  subtype5  6  2
  subtype6  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    6
  subtype2    8    4
  subtype3   12    4
  subtype4   12    6
  subtype5    6    2
  subtype6    4    0
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  TUMOR FREE        9        8       12       12        6        4
  WITH TUMOR        6        4        4        6        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       1      2       1            39       2
  subtype2       0      2       2            26       2
  subtype3       0      3       0            31       4
  subtype4       0      0       3            36       3
  subtype5       0      4       1            26       0
  subtype6       0      0       0            11       1
D2V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NIGERIA              1        0        0        0        0        0
  RUSSIA               2        2        3        0        4        0
  UKRAINE              1        2        0        3        1        0
  UNITED STATES       39       26       31       36       26       11
  VIETNAM              2        2        4        3        0        1
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 20 18  0  1
  subtype2  1 15 15  0  1
  subtype3  2 20 16  0  0
  subtype4  1 17 20  1  1
  subtype5  3 17  9  0  1
  subtype6  1  5  5  0  1
D2V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  G1        6        1        2        1        3        1
  G2       20       15       20       17       17        5
  G3       18       15       16       20        9        5
  G4        0        0        0        1        0        0
  GX        1        1        0        1        1        1
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V16, continuous
D2V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           3
  subtype2                                           3
  subtype3                                           5
  subtype4                                           5
  subtype5                                           5
  subtype6                                           4
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
  subtype4                                      0
  subtype5                                      3
  subtype6                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             10
  subtype2                                               1              6
  subtype3                                               0              8
  subtype4                                               1             10
  subtype5                                               1              6
  subtype6                                               0              3
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  25
  subtype2                  16
  subtype3                  19
  subtype4                  16
  subtype5                   9
  subtype6                   4
D2V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3        3        5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        0
  CURRENT SMOKER                                        10        6        8
  LIFELONG NON-SMOKER                                   25       16       19
                                                 clus
vv                                                subtype4 subtype5 subtype6
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            5        5        4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        3        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        1        0
  CURRENT SMOKER                                        10        6        3
  LIFELONG NON-SMOKER                                   16        9        4
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       13             1        0        1
  subtype2           3        6             0        1        2
  subtype3           5        7             3        0        0
  subtype4           5       10             4        0        3
  subtype5           1        5             5        0        1
  subtype6           1        3             1        0        1
D2V20, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMBINATION          3        3        5        5        1        1
  EXTERNAL            13        6        7       10        5        3
  EXTERNAL BEAM        1        0        3        4        5        1
  IMPLANTS             0        1        0        0        0        0
  INTERNAL             1        2        0        3        1        1
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V21, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 1 0
  subtype3 3 1
  subtype4 5 2
  subtype5 2 0
  subtype6 1 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    1    0
  subtype3    3    1
  subtype4    5    2
  subtype5    2    0
  subtype6    1    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CGY        4        1        3        5        2        1
  GY         0        0        1        2        0        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
D2V26, continuous
D2V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            1
  subtype2    1    0            0
  subtype3    0    0            0
  subtype4    0    1            0
  subtype5    0    0            0
  subtype6    0    0            0
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                  8
  subtype2                                                  8
  subtype3                                                  8
  subtype4                                                  5
  subtype5                                                  8
  subtype6                                                  4
D2V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        1        0
  2010                                                      0        0        0
  COMMON ILIAC                                              1        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        8        8        8
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  2003                                                      0        0        0
  2010                                                      1        0        0
  COMMON ILIAC                                              0        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        5        8        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   1
  subtype6                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       0
  subtype2                                   1                       2
  subtype3                                   0                       4
  subtype4                                   2                       3
  subtype5                                   3                       3
  subtype6                                   0                       1
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       0                       1
  subtype3                       0                       2
  subtype4                       1                       1
  subtype5                       0                       1
  subtype6                       0                       0
D2V29, multiclass
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        4        6        7        8        1 
 [1] "subtype5" "subtype4" "subtype5" "subtype3" "subtype4" "subtype2"
 [7] "subtype3" "subtype5" "subtype2" "subtype4" "subtype3" "subtype2"
[13] "subtype5" "subtype4" "subtype3" "subtype5" "subtype4" "subtype3"
[19] "subtype5" "subtype5" "subtype1" "subtype1" "subtype3" "subtype4"
[25] "subtype1" "subtype2" "subtype5" "subtype4"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0        2
  OTHER LOCATION, SPECIFY                    0        2        4        3
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    1        1        2        1
                                     clus
vv                                    subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        3
  OTHER LOCATION, SPECIFY                    3
  POSITIVE BLADDER MARGIN                    0
  POSITIVE VAGINAL MARGIN                    1
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             1
  subtype6                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              3
  subtype2                                              2
  subtype3                                              3
  subtype4                                              1
  subtype5                                              0
  subtype6                                              1
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                10
  subtype2                                                                                12
  subtype3                                                                                14
  subtype4                                                                                 3
  subtype5                                                                                13
  subtype6                                                                                 6
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           24
  subtype2                                                                                           11
  subtype3                                                                                           16
  subtype4                                                                                           21
  subtype5                                                                                            9
  subtype6                                                                                            4
D2V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       24
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       11
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       21
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        9
                                                                                              clus
vv                                                                                             subtype6
  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)        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V31, binary
          cls
clus        0  1
  subtype1 16 18
  subtype2  6 12
  subtype3 10 13
  subtype4 10  8
  subtype5 11 12
  subtype6  3  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   18
  subtype2    6   12
  subtype3   10   13
  subtype4   10    8
  subtype5   11   12
  subtype6    3    3
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        16        6       10       10       11        3
  PRESENT       18       12       13        8       12        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V32, continuous
D2V33, continuous
D2V34, binary
          cls
clus        0  1
  subtype1  0 13
  subtype2  5 18
  subtype3 10 20
  subtype4 14 17
  subtype5 12 13
  subtype6  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   13
  subtype2    5   18
  subtype3   10   20
  subtype4   14   17
  subtype5   12   13
  subtype6    2    7
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0        5       10       14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       13       18       20       17
                                          clus
vv                                         subtype5 subtype6
  KERATINIZING SQUAMOUS CELL CARCINOMA           12        2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       13        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     2                   31                   2
  subtype2     0                   21                   0
  subtype3     0                   28                   1
  subtype4     0                   20                   2
  subtype5     0                   23                   0
  subtype6     1                    6                   0
D2V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  OTHER                       2        0        0        0        0        1
  RADICAL HYSTERECTOMY       31       21       28       20       23        6
  SIMPLE HYSTERECTOMY         2        0        1        2        0        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          13         10
  subtype2            1           7          8
  subtype3            1           6         10
  subtype4            1           8          7
  subtype5            0           3          9
  subtype6            0           3          3
D2V37, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CURRENT USER        5        1        1        1        0        0
  FORMER USER        13        7        6        8        3        3
  NEVER USED         10        8       10        7        9        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V38, continuous
D2V39, binary
          cls
clus        0  1
  subtype1 24  4
  subtype2 14  1
  subtype3 13  4
  subtype4 13  1
  subtype5 14  5
  subtype6  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    4
  subtype2   14    1
  subtype3   13    4
  subtype4   13    1
  subtype5   14    5
  subtype6    3    0
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        24       14       13       13       14        3
  PRESENT        4        1        4        1        5        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V40, binary
          cls
clus       0 1
  subtype1 0 2
  subtype2 1 1
  subtype3 1 5
  subtype4 0 7
  subtype5 1 2
  subtype6 0 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    2
  subtype2    1    1
  subtype3    1    5
  subtype4    0    7
  subtype5    1    2
  subtype6    0    0
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  CARBOPLATIN        0        1        1        0        1
  CISPLATIN          2        1        5        7        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V41, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype5"              
[4] "subtype6"              
clus
subtype2 subtype3 subtype4 subtype5 subtype6 
       1        3        3        2        1 
[1] "subtype4" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0    0   1   18    6  0   2    3    3   4   1  0   0  0
  subtype2   1    0   4    8    5  1   1    0    1   2   0  0   0  3
  subtype3   1    0   7   13    2  2   1    2    1   3   0  1   0  0
  subtype4   0    0   8    7    3  0   1    1    2   3   0  1   1  3
  subtype5   0    1   6    6    5  0   1    1    1   1   1  0   0  1
  subtype6   0    0   0    3    3  0   0    0    1   1   0  0   0  1
D2V42, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1A         0        1        1        0        0        0
  T1A1        0        0        0        0        1        0
  T1B         1        4        7        8        6        0
  T1B1       18        8       13        7        6        3
  T1B2        6        5        2        3        5        3
  T2          0        1        2        0        0        0
  T2A         2        1        1        1        1        0
  T2A1        3        0        2        1        1        0
  T2A2        3        1        1        2        1        1
  T2B         4        2        3        3        1        1
  T3B         1        0        0        0        1        0
  T4          0        0        1        1        0        0
  TIS         0        0        0        1        0        0
  TX          0        3        0        3        1        1
[1] 14  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V43, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 62 13
  subtype2 32 12
  subtype3 46  8
subtype1 subtype2 subtype3 
      75       44       54 
subtype1 subtype2 subtype3 
      13       12        8 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       49.48        68.84        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MH 
       82.85        19.86        67.46        46.32        30.21        38.99 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
        2.43         3.58       100.14        20.42       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-DR-A0ZL TCGA-DR-A0ZM 
      134.33        15.48        73.41        85.55        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        22.98        16.83        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
        1.32         0.82         0.62         2.66        13.05         1.18 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R 
       12.66         0.26        13.91         0.69        13.58        13.48 
TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EK-A2RO 
       88.08         0.53         0.07         4.04         0.10         0.07 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ 
       20.35        23.84         0.92         0.66         1.45         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        0.82         3.52         1.97        21.67        20.78        14.93 
TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AU 
      117.40        36.36        19.33        20.48         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF 
        0.89         0.82        13.87         0.03         5.42         4.34 
TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-UC-A7PF 
        3.45         5.75        93.99 

$subtype2
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A2LT 
       57.04        11.44        18.74         5.46        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC 
       73.45        83.05        78.35        52.01        25.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DS-A0VM TCGA-DS-A0VN 
       60.69        94.95         9.34        13.61       117.99       118.65 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3Y4 TCGA-EA-A43B 
       28.31        12.36         8.28         0.76        14.50         1.81 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ 
       12.59        45.96         6.64         0.36         1.18         0.10 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3TX TCGA-IR-A3LH TCGA-IR-A3LK 
        0.03         6.94         4.47         1.48        78.71        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL TCGA-LP-A4AX TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       14.43        16.64        15.58         0.07         5.85         3.39 
TCGA-R2-A69V TCGA-UC-A7PD 
       19.59        11.67 

$subtype3
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       23.67        31.40        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
        0.46        44.22        38.43         0.82        18.02        17.85 
TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-DS-A1OD TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 
        9.67         2.73       127.36        16.18         7.33         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZE 
        1.35        14.50        12.82        14.89         1.48        14.99 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 
       14.96         0.59        23.70         2.24         0.10         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J 
       14.70         6.12         1.22         2.17         1.02         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
        1.32         1.12        25.41         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A69B TCGA-MY-A5BD TCGA-MY-A5BE 
       66.81        96.95        81.96        10.06        29.72         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        2.96         3.72         3.72         4.80         6.25         3.88 

subtype1 subtype2 subtype3 
    0.03     0.03     0.07 
subtype1 subtype2 subtype3 
  182.93   118.65   147.39 
subtype1 subtype2 subtype3 
  13.870   14.465    9.865 
[1] "0.0 - 182.9 (13.9)" "0.0 - 118.7 (14.5)" "0.1 - 147.4 (9.9)" 
D3V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 40 19     2
  subtype2 25  7     0
  subtype3 35 11     1
D3V3, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          40       25       35
  T2          19        7       11
  T3+T4        2        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus        0  1
  subtype1 31 26
  subtype2 23  7
  subtype3 35  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   26
  subtype2   23    7
  subtype3   35    9
   clus
vv  subtype1 subtype2 subtype3
  0       31       23       35
  1       26        7        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 29  0 33
  subtype2 20  0 14
  subtype3 27  3 18
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       29       20       27
  M1        0        0        3
  MX       33       14       18
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             0                               77
  subtype2             0                               47
  subtype3             2                               24
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             0
  subtype2                                             0
  subtype3                                             4
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                  20
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         2
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            0
  subtype2                                            0
  subtype3                                            4
D3V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        0        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    77       47       24
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        0       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0        4
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 14 63
  subtype2 10 37
  subtype3  6 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   63
  subtype2   10   37
  subtype3    6   50
     clus
vv    subtype1 subtype2 subtype3
  NO        14       10        6
  YES       63       37       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                         8
  subtype2                                4     3                         6
  subtype3                                0     4                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    56
  subtype2                                         1    32
  subtype3                                         0    47
D3V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 2        4        0
  ASIAN                                            8        3        4
  BLACK OR AFRICAN AMERICAN                        8        6        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           56       32       47
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus        0  1
  subtype1  3 56
  subtype2  4 32
  subtype3  5 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   56
  subtype2    4   32
  subtype3    5   41
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        4        5
  NOT HISPANIC OR LATINO       56       32       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
D3V13, binary
          cls
clus        0  1
  subtype1 22  8
  subtype2 13  6
  subtype3 15  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    8
  subtype2   13    6
  subtype3   15    6
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       22       13       15
  WITH TUMOR        8        6        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       0      7       2            61       7
  subtype2       0      1       2            42       2
  subtype3       1      3       2            47       3
D3V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  NIGERIA              0        0        1
  RUSSIA               7        1        3
  UKRAINE              2        2        2
  UNITED STATES       61       42       47
  VIETNAM              7        2        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 44 26  0  1
  subtype2  2 17 25  1  1
  subtype3  6 24 23  0  3
D3V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        2        6
  G2       44       17       24
  G3       26       25       23
  G4        0        1        0
  GX        1        1        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V16, continuous
D3V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          11
  subtype2                                           4
  subtype3                                           8
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      7
  subtype2                                      0
  subtype3                                      1
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             16
  subtype2                                               0             10
  subtype3                                               0             10
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  33
  subtype2                  21
  subtype3                  29
D3V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           11        4        8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 7        0        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0        0
  CURRENT SMOKER                                        16       10       10
  LIFELONG NON-SMOKER                                   33       21       29
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           8       13             7        2
  subtype2           5       11             5        2
  subtype3           4       13             2        1
D3V20, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          8        5        4
  EXTERNAL            13       11       13
  EXTERNAL BEAM        7        5        2
  INTERNAL             2        2        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V21, binary
          cls
clus       0 1
  subtype1 4 1
  subtype2 5 1
  subtype3 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    5    1
  subtype3    3    1
     clus
vv    subtype1 subtype2 subtype3
  CGY        4        5        3
  GY         1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
D3V26, continuous
D3V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            0
  subtype2    1    1            0
  subtype3    0    0            1
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                 23
  subtype2                                                  6
  subtype3                                                 10
D3V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        1        0
  2010                                                      0        1        0
  COMMON ILIAC                                              0        0        1
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)       23        6       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       6
  subtype2                                   2                       5
  subtype3                                   2                       1
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       2
  subtype2                       0                       2
  subtype3                       0                       1
D3V29, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        2
  OTHER LOCATION, SPECIFY                    6        5        1
  POSITIVE BLADDER MARGIN                    1        0        0
  POSITIVE VAGINAL MARGIN                    2        2        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             2
  subtype2                                             0
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              4
  subtype2                                              2
  subtype3                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                30
  subtype2                                                                                 9
  subtype3                                                                                14
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           30
  subtype2                                                                                           22
  subtype3                                                                                           29
D3V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       30
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  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)       22
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       29
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V31, binary
          cls
clus        0  1
  subtype1 21 31
  subtype2 12 10
  subtype3 21 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   31
  subtype2   12   10
  subtype3   21   21
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        21       12       21
  PRESENT       31       10       21
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V32, continuous
D3V33, continuous
D3V34, binary
          cls
clus        0  1
  subtype1 21 38
  subtype2 16 23
  subtype3  2 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   38
  subtype2   16   23
  subtype3    2   20
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           21       16        2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       38       23       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     1                   55                   1
  subtype2     0                   23                   2
  subtype3     2                   39                   2
D3V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3
  OTHER                       1        0        2
  RADICAL HYSTERECTOMY       55       23       39
  SIMPLE HYSTERECTOMY         1        2        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            1          12         22
  subtype2            2          11         10
  subtype3            5          17         11
D3V37, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        1        2        5
  FORMER USER        12       11       17
  NEVER USED         22       10       11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V38, continuous
D3V39, binary
          cls
clus        0  1
  subtype1 30  8
  subtype2 18  0
  subtype3 30  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    8
  subtype2   18    0
  subtype3   30    6
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        30       18       30
  PRESENT        8        0        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V40, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 1 7
  subtype3 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    1    7
  subtype3    0    3
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        1        1        0
  CISPLATIN          6        7        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V41, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 
       7        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  subtype1   2    1  14   16    7  2   3    2    4   8   1  1  2
  subtype2   0    0   8   11    6  1   1    2    2   1   0  0  4
  subtype3   0    0   1   25    9  0   2    2    3   4   1  0  1
D3V42, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         2        0        0
  T1A1        1        0        0
  T1B        14        8        1
  T1B1       16       11       25
  T1B2        7        6        9
  T2          2        1        0
  T2A         3        1        2
  T2A1        2        2        2
  T2A2        4        2        3
  T2B         8        1        4
  T3B         1        0        1
  T4          1        0        0
  TX          2        4        1
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V43, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 70 16
  subtype2 22  3
  subtype3 10  7
  subtype4 38  7
subtype1 subtype2 subtype3 subtype4 
      86       25       17       45 
subtype1 subtype2 subtype3 subtype4 
      16        3        7        7 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        57.04        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LY TCGA-C5-A2LZ 
       38.99         2.43        40.93         3.58        78.35       100.14 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL 
       73.41        85.55        60.69        94.95        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ 
       58.88         2.66       118.65        28.31        12.36        22.98 
TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       16.83        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD 
        2.66         1.18        12.66         0.26        13.91         0.69 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PG 
       13.48        12.59        45.96         6.64        88.08         0.53 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.07         4.04         0.36         0.10         0.07         0.10 
TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       20.35         0.92         0.66         1.58         0.82         3.52 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
        1.97        25.41        14.93        26.56        36.36        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A5U3 
       19.33        20.48        15.58         5.13         0.10         0.82 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
       13.87         5.42         4.34         3.45         3.39         5.75 
TCGA-R2-A69V TCGA-UC-A7PF 
       19.59        93.99 

$subtype2
TCGA-BI-A20A TCGA-C5-A2LX TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A1OD TCGA-EA-A1QS 
       23.67        83.05        36.76       117.99       127.36         0.76 
TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EK-A3GN TCGA-EX-A69L 
       13.05         1.35        14.99        13.58         0.03         4.47 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TX TCGA-HM-A3JJ TCGA-HM-A3JK 
        6.12        23.84         1.45         1.48        21.67        20.78 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-LP-A4AW TCGA-MU-A5YI TCGA-MY-A5BE TCGA-Q1-A5R3 
      147.39       117.40         0.89         0.03         0.07         5.85 
TCGA-RA-A741 
        3.88 

$subtype3
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD 
       11.44        18.74         5.46        73.18        73.45        52.01 
TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2RJ 
       17.19         9.34         8.28        14.50         1.81         1.18 
TCGA-EX-A3L1 TCGA-IR-A3LH TCGA-JW-A5VG TCGA-LP-A4AX TCGA-UC-A7PD 
        6.94        78.71        14.43         0.07        11.67 

$subtype4
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       31.40        35.01        57.73        53.16        35.61         0.46 
TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM 
       44.22        38.43         0.82        18.02        17.85         9.67 
TCGA-C5-A7X8 TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA 
        2.73        16.18         7.33         1.35        14.50        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RL TCGA-EK-A2RM 
       14.89         1.48        14.96         0.59        23.70         2.24 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
        0.10         7.92        14.70         1.22         2.17         1.02 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.35         1.32         1.12         4.11       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A69B TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 
       96.95        81.96        10.06        29.72         2.96         3.72 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
        3.72         4.80         6.25 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.03     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  182.93   147.39    78.71   137.16 
subtype1 subtype2 subtype3 subtype4 
   15.53    13.05    11.67     9.67 
[1] "0.1 - 182.9 (15.5)" "0.0 - 147.4 (13.1)" "0.1 - 78.7 (11.7)" 
[4] "0.1 - 137.2 (9.7)" 
D4V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 45 19     2
  subtype2 19  3     0
  subtype3  9  4     0
  subtype4 27 11     1
D4V3, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          45       19        9       27
  T2          19        3        4       11
  T3+T4        2        0        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus        0  1
  subtype1 39 22
  subtype2 13  8
  subtype3 10  3
  subtype4 27  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   22
  subtype2   13    8
  subtype3   10    3
  subtype4   27    9
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       39       13       10       27
  1       22        8        3        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 33  0 34
  subtype2 15  0  8
  subtype3  8  0  6
  subtype4 20  3 17
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       33       15        8       20
  M1        0        0        0        3
  MX       34        8        6       17
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             0                               91
  subtype2             0                               25
  subtype3             0                               17
  subtype4             2                               15
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             0
  subtype2                                             0
  subtype3                                             0
  subtype4                                             4
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   0
  subtype4                                  20
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         0
  subtype4                                         2
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            0
  subtype2                                            0
  subtype3                                            0
  subtype4                                            4
D4V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    91       25       17
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0        0
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         4
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 17 74
  subtype2  4 21
  subtype3  4 13
  subtype4  5 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   74
  subtype2    4   21
  subtype3    4   13
  subtype4    5   42
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17        4        4        5
  YES       74       21       13       42
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                4     7                         9
  subtype2                                0     4                         3
  subtype3                                2     1                         3
  subtype4                                0     3                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    67
  subtype2                                         0    17
  subtype3                                         0    11
  subtype4                                         0    40
D4V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 4        0        2        0
  ASIAN                                            7        4        1        3
  BLACK OR AFRICAN AMERICAN                        9        3        3        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           67       17       11       40
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
          cls
clus        0  1
  subtype1  6 63
  subtype2  0 20
  subtype3  1 12
  subtype4  5 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   63
  subtype2    0   20
  subtype3    1   12
  subtype4    5   34
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            6        0        1        5
  NOT HISPANIC OR LATINO       63       20       12       34
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
D4V13, binary
          cls
clus        0  1
  subtype1 23  9
  subtype2 12  1
  subtype3  5  4
  subtype4 10  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    9
  subtype2   12    1
  subtype3    5    4
  subtype4   10    6
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       23       12        5       10
  WITH TUMOR        9        1        4        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       0      7       2            76       6
  subtype2       0      2       0            20       3
  subtype3       0      0       2            14       1
  subtype4       1      2       2            40       2
D4V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  NIGERIA              0        0        0        1
  RUSSIA               7        2        0        2
  UKRAINE              2        0        2        2
  UNITED STATES       76       20       14       40
  VIETNAM              6        3        1        2
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 52 30  0  2
  subtype2  1  6 17  0  1
  subtype3  1  5 10  1  0
  subtype4  6 22 17  0  2
D4V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        6        1        1        6
  G2       52        6        5       22
  G3       30       17       10       17
  G4        0        0        1        0
  GX        2        1        0        2
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V16, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      12        6        2        5 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype4"
 [7] "subtype1" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
D4V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          10
  subtype2                                           7
  subtype3                                           2
  subtype4                                           4
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      6
  subtype2                                      1
  subtype3                                      0
  subtype4                                      1
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             20
  subtype2                                               0              2
  subtype3                                               0              5
  subtype4                                               0              9
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  37
  subtype2                  12
  subtype3                   8
  subtype4                  26
D4V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           10        7        2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 6        1        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0        0
  CURRENT SMOKER                                        20        2        5
  LIFELONG NON-SMOKER                                   37       12        8
                                                 clus
vv                                                subtype4
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0
  CURRENT SMOKER                                         9
  LIFELONG NON-SMOKER                                   26
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1          10       14             7        3
  subtype2           1        5             4        1
  subtype3           2        6             2        1
  subtype4           4       12             1        0
D4V20, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  COMBINATION         10        1        2        4
  EXTERNAL            14        5        6       12
  EXTERNAL BEAM        7        4        2        1
  INTERNAL             3        1        1        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V21, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 2 1
  subtype3 4 0
  subtype4 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    2    1
  subtype3    4    0
  subtype4    3    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  CGY        3        2        4        3
  GY         2        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
D4V26, continuous
D4V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    1            0
  subtype2    1    0            0
  subtype3    0    0            0
  subtype4    0    0            1
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                 21
  subtype2                                                  7
  subtype3                                                  3
  subtype4                                                  8
D4V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        1        0
  2010                                                      1        0        0
  COMMON ILIAC                                              0        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)       21        7        3
                                                    clus
vv                                                   subtype4
  2003                                                      0
  2010                                                      0
  COMMON ILIAC                                              1
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   3                       9
  subtype2                                   1                       2
  subtype3                                   1                       1
  subtype4                                   1                       0
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       1
  subtype2                       0                       2
  subtype3                       0                       1
  subtype4                       0                       1
D4V29, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        3        1        1        1
  OTHER LOCATION, SPECIFY                    9        2        1        0
  POSITIVE BLADDER MARGIN                    1        0        0        0
  POSITIVE VAGINAL MARGIN                    1        2        1        1
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             2
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              3
  subtype2                                              3
  subtype3                                              1
  subtype4                                              3
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                30
  subtype2                                                                                12
  subtype3                                                                                 0
  subtype4                                                                                11
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           37
  subtype2                                                                                            8
  subtype3                                                                                           11
  subtype4                                                                                           25
D4V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        8
                                                                                              clus
vv                                                                                             subtype3
  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)                   0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       11
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       25
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V31, binary
          cls
clus        0  1
  subtype1 23 28
  subtype2  8 12
  subtype3  5  5
  subtype4 18 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   28
  subtype2    8   12
  subtype3    5    5
  subtype4   18   17
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        23        8        5       18
  PRESENT       28       12        5       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V32, continuous
D4V33, continuous
D4V34, binary
          cls
clus        0  1
  subtype1 27 46
  subtype2  6 13
  subtype3  5  8
  subtype4  1 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   46
  subtype2    6   13
  subtype3    5    8
  subtype4    1   14
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA           27        6        5        1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       46       13        8       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     1                   56                   1
  subtype2     0                   19                   0
  subtype3     0                    9                   2
  subtype4     2                   33                   2
D4V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3 subtype4
  OTHER                       1        0        0        2
  RADICAL HYSTERECTOMY       56       19        9       33
  SIMPLE HYSTERECTOMY         1        0        2        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            0          15         22
  subtype2            1           8          6
  subtype3            2           3          6
  subtype4            5          14          9
D4V37, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        0        1        2        5
  FORMER USER        15        8        3       14
  NEVER USED         22        6        6        9
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V38, continuous
D4V39, binary
          cls
clus        0  1
  subtype1 35  8
  subtype2 11  2
  subtype3  6  0
  subtype4 26  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    8
  subtype2   11    2
  subtype3    6    0
  subtype4   26    4
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        35       11        6       26
  PRESENT        8        2        0        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V40, binary
          cls
clus       0 1
  subtype1 2 8
  subtype2 0 3
  subtype3 0 3
  subtype4 0 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    8
  subtype2    0    3
  subtype3    0    3
  subtype4    0    2
             clus
vv            subtype1 subtype2 subtype3 subtype4
  CARBOPLATIN        2        0        0        0
  CISPLATIN          8        3        3        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V41, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       7        1        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  subtype1   1    0  16   16   12  2   3    1    5   8   1  1  3
  subtype2   1    1   0   15    2  1   0    1    0   1   0  0  2
  subtype3   0    0   6    2    1  0   1    2    1   0   0  0  1
  subtype4   0    0   1   19    7  0   2    2    3   4   1  0  1
D4V42, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4
  T1A         1        1        0        0
  T1A1        0        1        0        0
  T1B        16        0        6        1
  T1B1       16       15        2       19
  T1B2       12        2        1        7
  T2          2        1        0        0
  T2A         3        0        1        2
  T2A1        1        1        2        2
  T2A2        5        0        1        3
  T2B         8        1        0        4
  T3B         1        0        0        1
  T4          1        0        0        0
  TX          3        2        1        1
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V43, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 51 10
  subtype2 48  9
  subtype3 56 19
subtype1 subtype2 subtype3 
      61       57       75 
subtype1 subtype2 subtype3 
      10        9       19 
$subtype1
TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       82.85        31.40        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       35.61         0.46        33.90        44.22        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-C5-A902 
       18.02       182.93         9.67         2.73        27.52         4.90 
TCGA-C5-A905 TCGA-DS-A1OD TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A410 
      160.41       127.36        16.18         8.28        13.05         1.35 
TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZF 
       14.50        12.82        14.89         1.48        13.91        14.96 
TCGA-EA-A6QX TCGA-EK-A2IR TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
       13.58        88.08         0.59         1.18        23.70         2.24 
TCGA-EK-A3GK TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        0.10        14.70         4.47         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 
       23.84         1.02         1.35         1.32         1.12         4.11 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LI TCGA-JW-A5VK TCGA-JW-A69B TCGA-MY-A5BD 
      137.16        66.81        81.96        20.48        10.06        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P 
        0.07         4.34         2.96         3.72         3.72         4.80 
TCGA-Q1-A73R 
        6.25 

$subtype2
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1M5 TCGA-C5-A1MP TCGA-C5-A3HF 
       49.48        23.67        68.84        67.46         3.58        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7XC 
       20.42       101.82       134.33        73.41        85.55        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-DR-A0ZM 
        8.35        75.78         6.12        20.91        17.03        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS 
       36.76         2.66        28.90        16.83         7.33         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S 
        1.74         1.32         0.82         0.62         1.35        12.66 
TCGA-EA-A50E TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2RC 
        0.26         0.69        14.99        13.48         0.36         4.04 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX 
        0.07        20.35         7.92         2.17         1.45         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        0.82         3.52        25.41        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-LP-A4AW TCGA-MU-A51Y 
      147.39       117.40        96.95        78.71         0.89        13.87 
TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-UC-A7PF 
        0.03         3.45        93.99 

$subtype3
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        11.44        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK 
      173.29         5.46        19.86        46.32        38.99         2.43 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI 
       52.01        25.35        15.48        17.19        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A907 
        9.34        13.61        45.83        99.91        23.51         4.47 
TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OC 
       87.75       117.99       118.65         8.75        28.31        12.36 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B 
       22.98        12.36         2.66         1.18        14.50         1.81 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RD 
       12.59        45.96         6.64         0.53         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-FU-A2QG 
        0.36         0.10         0.10         0.03         6.94         0.92 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
        0.66         1.58         1.97        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX 
       16.64        19.33        15.58         5.13         0.10         0.07 
TCGA-LP-A5U3 TCGA-MU-A8JM TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        0.82         5.42         5.49         5.85         3.39         5.75 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       19.59         3.88        11.67 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  182.93   147.39   177.04 
subtype1 subtype2 subtype3 
   13.05    14.93    14.43 
[1] "0.1 - 182.9 (13.1)" "0.0 - 147.4 (14.9)" "0.0 - 177.0 (14.4)"
D5V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 38 16     1
  subtype2 34 12     1
  subtype3 36 11     2
D5V3, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          38       34       36
  T2          16       12       11
  T3+T4        1        1        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus        0  1
  subtype1 38 13
  subtype2 30 16
  subtype3 32 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   13
  subtype2   30   16
  subtype3   32   15
   clus
vv  subtype1 subtype2 subtype3
  0       38       30       32
  1       13       16       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 28  3 25
  subtype2 28  0 21
  subtype3 27  1 24
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       28       28       27
  M1        3        0        1
  MX       25       21       24
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               36
  subtype2             0                               54
  subtype3             0                               78
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             3
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  16
  subtype2                                   4
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            3
  subtype2                                            1
  subtype3                                            0
D5V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    36       54       78
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        3        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 16        4        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         3        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  8 54
  subtype2  8 52
  subtype3 16 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   54
  subtype2    8   52
  subtype3   16   62
     clus
vv    subtype1 subtype2 subtype3
  NO         8        8       16
  YES       54       52       62
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         8
  subtype2                                1     6                         6
  subtype3                                6     5                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    48
  subtype2                                         0    44
  subtype3                                         1    56
D5V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        6
  ASIAN                                            5        6        5
  BLACK OR AFRICAN AMERICAN                        8        6        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           48       44       56
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
          cls
clus        0  1
  subtype1  4 47
  subtype2  2 42
  subtype3  7 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   47
  subtype2    2   42
  subtype3    7   55
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        7
  NOT HISPANIC OR LATINO       47       42       55
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
D5V13, binary
          cls
clus        0  1
  subtype1 19  6
  subtype2 12  6
  subtype3 20 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    6
  subtype2   12    6
  subtype3   20   10
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       19       12       20
  WITH TUMOR        6        6       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       1      2       3            53       3
  subtype2       0      6       2            47       5
  subtype3       0      3       2            69       4
D5V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  NIGERIA              1        0        0
  RUSSIA               2        6        3
  UKRAINE              3        2        2
  UNITED STATES       53       47       69
  VIETNAM              3        5        4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 24 30  0  2
  subtype2  6 34 18  1  0
  subtype3  2 36 35  0  3
D5V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        6        2
  G2       24       34       36
  G3       30       18       35
  G4        0        1        0
  GX        2        0        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V16, continuous
D5V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  subtype2                                           7
  subtype3                                          11
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      4
  subtype3                                      2
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              8
  subtype2                                               2             15
  subtype3                                               1             20
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  35
  subtype2                  26
  subtype3                  28
D5V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        7       11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        4        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                         8       15       20
  LIFELONG NON-SMOKER                                   35       26       28
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           5       16             3        0        0
  subtype2           3       13             5        1        3
  subtype3          10       15             6        0        5
D5V20, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          5        3       10
  EXTERNAL            16       13       15
  EXTERNAL BEAM        3        5        6
  IMPLANTS             0        1        0
  INTERNAL             0        3        5
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V21, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 6 0
  subtype3 6 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    6    0
  subtype3    6    4
     clus
vv    subtype1 subtype2 subtype3
  CGY        4        6        6
  GY         0        0        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
D5V26, continuous
D5V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            1
  subtype2    0    0            0
  subtype3    1    1            0
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                 12
  subtype2                                                 16
  subtype3                                                 13
D5V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        0        1
  2010                                                      0        0        1
  COMMON ILIAC                                              1        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)       12       16       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       1
  subtype2                                   2                       5
  subtype3                                   3                       7
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       1                       3
  subtype3                       0                       2
D5V29, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        3
  OTHER LOCATION, SPECIFY                    1        5        7
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    1        3        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             1
  subtype2                                             1
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              4
  subtype2                                              3
  subtype3                                              3
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                14
  subtype2                                                                                23
  subtype3                                                                                21
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           28
  subtype2                                                                                           22
  subtype3                                                                                           35
D5V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       28
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       22
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       35
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V31, binary
          cls
clus        0  1
  subtype1 17 28
  subtype2 20 22
  subtype3 19 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   28
  subtype2   20   22
  subtype3   19   16
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        17       20       19
  PRESENT       28       22       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V32, continuous
D5V33, continuous
D5V34, binary
          cls
clus        0  1
  subtype1  4 25
  subtype2 14 27
  subtype3 25 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   25
  subtype2   14   27
  subtype3   25   36
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            4       14       25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       25       27       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     3                   46                   1
  subtype2     0                   47                   1
  subtype3     0                   36                   3
D5V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3
  OTHER                       3        0        0
  RADICAL HYSTERECTOMY       46       47       36
  SIMPLE HYSTERECTOMY         1        1        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            4          13         16
  subtype2            2          13         15
  subtype3            2          14         16
D5V37, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        4        2        2
  FORMER USER        13       13       14
  NEVER USED         16       15       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V38, continuous
D5V39, binary
          cls
clus        0  1
  subtype1 28  6
  subtype2 27  7
  subtype3 26  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    6
  subtype2   27    7
  subtype3   26    2
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        28       27       26
  PRESENT        6        7        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V40, binary
          cls
clus        0  1
  subtype1  0  4
  subtype2  1  3
  subtype3  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype2    1    3
  subtype3    2   10
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        2
  CISPLATIN          4        3       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V41, continuous
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0    0   6   21   11  1   2    4    5   4   1  0   0  1
  subtype2   1    1   5   20    7  0   3    2    2   5   0  1   0  2
  subtype3   1    0  15   14    6  2   1    1    2   5   1  1   1  5
D5V42, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        1        1
  T1A1        0        1        0
  T1B         6        5       15
  T1B1       21       20       14
  T1B2       11        7        6
  T2          1        0        2
  T2A         2        3        1
  T2A1        4        2        1
  T2A2        5        2        2
  T2B         4        5        5
  T3B         1        0        1
  T4          0        1        1
  TIS         0        0        1
  TX          1        2        5
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V43, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 29  7
  subtype2 95 23
  subtype3 31  8
subtype1 subtype2 subtype3 
      36      118       39 
subtype1 subtype2 subtype3 
       7       23        8 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS 
       31.40        35.01        57.73        35.61         0.46        44.22 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT 
       38.43         0.82        17.85         9.67         2.73         6.12 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EK-A2RL 
       16.18         7.33        14.50        12.82         1.48        23.70 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO 
        0.10         7.92        14.70         4.73         1.22         2.17 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.35         1.32         1.12         4.11       137.16        66.81 
TCGA-IR-A3LF TCGA-JW-A69B TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
       96.95        10.06         3.72         3.72         4.80         6.25 

$subtype2
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        11.44        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85         5.46        19.86        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LV 
       53.16        38.99        40.93        33.90        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL 
       83.05        78.35       100.14        52.01        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      182.93        25.35        15.48        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95         9.34        13.61        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A902 
       99.91        23.51        27.52        20.91        17.03         4.90 
TCGA-C5-A905 TCGA-C5-A907 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN 
      160.41         4.47        87.75        58.88       117.99       118.65 
TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A7WI 
        8.75        28.31        12.36       127.36        22.98         8.28 
TCGA-EA-A3HR TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         2.66        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 
        1.35         1.81        12.66         0.26        14.89        13.91 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR 
       14.96        13.58        12.59        45.96         6.64        88.08 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.53         0.59         0.07         0.03         0.36         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 
        2.24         0.10         0.07         0.10         0.03         6.94 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.47         6.12        23.84         0.92         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A5XV TCGA-IR-A3LH TCGA-IR-A3LI 
        1.58         1.48         0.82         1.97        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A8JM 
       15.58         5.13         0.10         0.07         0.82         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       29.72         0.07         4.34         5.49         2.96         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-RA-A741 TCGA-UC-A7PD 
        3.39         5.75         3.88        11.67 

$subtype3
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-C5-A1MP 
       23.67        68.84       177.04        67.46         2.43         3.58 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7XC TCGA-DS-A0VK TCGA-DS-A0VL 
      101.82       134.33        73.41        50.99        36.76         2.66 
TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
       28.90        16.83         0.76        12.36         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2RC 
        0.62         0.69        14.99        13.48         0.36         4.04 
TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       20.35         1.45         3.52        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI 
       14.93       147.39       117.40         0.89        13.87         0.03 
TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PF 
        3.45        19.59        93.99 

subtype1 subtype2 subtype3 
    0.10     0.03     0.03 
subtype1 subtype2 subtype3 
  137.16   182.93   177.04 
subtype1 subtype2 subtype3 
   7.625   14.465   14.990 
[1] "0.1 - 137.2 (7.6)"  "0.0 - 182.9 (14.5)" "0.0 - 177.0 (15.0)"
D6V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 22  7     1
  subtype2 56 27     3
  subtype3 30  5     0
D6V3, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          22       56       30
  T2           7       27        5
  T3+T4        1        3        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 21  7
  subtype2 57 26
  subtype3 22 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    7
  subtype2   57   26
  subtype3   22   11
   clus
vv  subtype1 subtype2 subtype3
  0       21       57       22
  1        7       26       11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 13  2 16
  subtype2 49  2 39
  subtype3 21  0 15
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       13       49       21
  M1        2        2        0
  MX       16       39       15
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                                7
  subtype2             0                              121
  subtype3             0                               40
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  19
  subtype2                                   1
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         1
  subtype2                                         1
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            4
  subtype2                                            0
  subtype3                                            0
D6V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                     7      121       40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 19        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            1        1        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         4        0        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1   4  33
  subtype2  22 101
  subtype3   6  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   33
  subtype2   22  101
  subtype3    6   34
     clus
vv    subtype1 subtype2 subtype3
  NO         4       22        6
  YES       33      101       34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         2
  subtype2                                7     9                        16
  subtype3                                0     5                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    32
  subtype2                                         1    88
  subtype3                                         0    28
D6V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        7        0
  ASIAN                                            2        9        5
  BLACK OR AFRICAN AMERICAN                        2       16        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           32       88       28
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
          cls
clus        0  1
  subtype1  4 25
  subtype2  9 87
  subtype3  0 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   25
  subtype2    9   87
  subtype3    0   32
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        9        0
  NOT HISPANIC OR LATINO       25       87       32
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
D6V13, binary
          cls
clus        0  1
  subtype1  7  5
  subtype2 32 12
  subtype3 12  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2   32   12
  subtype3   12    5
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE        7       32       12
  WITH TUMOR        5       12        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       0      0       2            34       1
  subtype2       1      6       4           105       7
  subtype3       0      5       1            30       4
D6V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  NIGERIA              0        1        0
  RUSSIA               0        6        5
  UKRAINE              2        4        1
  UNITED STATES       34      105       30
  VIETNAM              1        7        4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  5 18 12  0  2
  subtype2  5 56 55  1  3
  subtype3  4 20 16  0  0
D6V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        5        5        4
  G2       18       56       20
  G3       12       55       16
  G4        0        1        0
  GX        2        3        0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V16, continuous
D6V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           3
  subtype2                                          19
  subtype3                                           3
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      3
  subtype3                                      4
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              9
  subtype2                                               2             26
  subtype3                                               1              8
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  21
  subtype2                  48
  subtype3                  20
D6V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3       19        3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        3        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                         9       26        8
  LIFELONG NON-SMOKER                                   21       48       20
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       10             1        0        1
  subtype2          12       27            10        0        6
  subtype3           3        7             3        1        1
D6V20, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          3       12        3
  EXTERNAL            10       27        7
  EXTERNAL BEAM        1       10        3
  IMPLANTS             0        0        1
  INTERNAL             1        6        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V21, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 9 3
  subtype3 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    9    3
  subtype3    3    1
     clus
vv    subtype1 subtype2 subtype3
  CGY        4        9        3
  GY         0        3        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
D6V26, continuous
D6V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            1
  subtype2    1    1            0
  subtype3    0    0            0
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                  7
  subtype2                                                 24
  subtype3                                                 10
D6V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        1        0
  2010                                                      0        1        0
  COMMON ILIAC                                              1        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        7       24       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       0
  subtype2                                   5                       9
  subtype3                                   2                       4
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       1                       4
  subtype3                       0                       1
D6V29, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       20        7 
 [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2"
                                     clus
vv                                    subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        5        2
  OTHER LOCATION, SPECIFY                    9        4
  POSITIVE BLADDER MARGIN                    1        0
  POSITIVE VAGINAL MARGIN                    4        1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             1
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              1
  subtype2                                              5
  subtype3                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 9
  subtype2                                                                                35
  subtype3                                                                                14
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           21
  subtype2                                                                                           48
  subtype3                                                                                           16
D6V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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)                   9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       21
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       48
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V31, binary
          cls
clus        0  1
  subtype1 15 13
  subtype2 30 33
  subtype3 11 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   13
  subtype2   30   33
  subtype3   11   20
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        15       30       11
  PRESENT       13       33       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V32, continuous
D6V33, continuous
D6V34, binary
          cls
clus        0  1
  subtype1  0  9
  subtype2 32 59
  subtype3 11 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2   32   59
  subtype3   11   20
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       32       11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        9       59       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     2                   24                   2
  subtype2     1                   69                   3
  subtype3     0                   36                   0
D6V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3
  OTHER                       2        1        0
  RADICAL HYSTERECTOMY       24       69       36
  SIMPLE HYSTERECTOMY         2        3        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            4          11          7
  subtype2            3          23         29
  subtype3            1           6         11
D6V37, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        4        3        1
  FORMER USER        11       23        6
  NEVER USED          7       29       11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V38, continuous
D6V39, binary
          cls
clus        0  1
  subtype1 21  2
  subtype2 40  9
  subtype3 20  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    2
  subtype2   40    9
  subtype3   20    4
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        21       40       20
  PRESENT        2        9        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V40, binary
          cls
clus        0  1
  subtype1  0  2
  subtype2  1 13
  subtype3  2  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    2
  subtype2    1   13
  subtype3    2    2
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        2
  CISPLATIN          2       13        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V41, continuous
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0    0   1   16    5  0   2    3    1   1   1  0   0  1
  subtype2   1    0  17   23   15  3   2    3    8  11   1  2   1  6
  subtype3   1    1   8   16    4  0   2    1    0   2   0  0   0  1
D6V42, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        1        1
  T1A1        0        0        1
  T1B         1       17        8
  T1B1       16       23       16
  T1B2        5       15        4
  T2          0        3        0
  T2A         2        2        2
  T2A1        3        3        1
  T2A2        1        8        0
  T2B         1       11        2
  T3B         1        1        0
  T4          0        2        0
  TIS         0        1        0
  TX          1        6        1
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V43, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 53 10
  subtype2 48 13
  subtype3 54 15
subtype1 subtype2 subtype3 
      63       61       69 
subtype1 subtype2 subtype3 
      10       13       15 
$subtype1
TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       82.85        31.40        30.21        35.01        57.73        53.16 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 
       35.61         0.46        44.22        83.05        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8XJ 
       18.02       182.93         9.67         2.73         8.35        75.78 
TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3QD 
       27.52         4.90       160.41        16.18         8.28        13.05 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        14.50        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IR TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RL 
       14.96        13.58        88.08         0.59         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        2.24         0.10        14.70         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A770 TCGA-HM-A6W2 
       23.84         2.17         1.02         1.35         1.12         4.11 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VK TCGA-JW-A69B 
      137.16        66.81        96.95        81.96        20.48        10.06 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV 
       29.72         0.07         4.34         2.96         3.72         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.75         4.80         6.25 

$subtype2
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1M5 TCGA-C5-A1MK 
       49.48        23.67        68.84        18.74        67.46         2.43 
TCGA-C5-A1MP TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
        3.58        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7XC TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 
       73.41        85.55        50.99         6.12        20.91        17.03 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OD TCGA-DS-A5RQ 
       58.88        36.76         8.75        28.90       127.36        16.83 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.62         1.35        12.66         0.26         0.69        14.99 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2RC TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A1H6 
       13.48         0.36         4.04         0.07        20.35         7.92 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-HG-A2PA 
        1.45         1.48         0.82         3.52         1.32        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH 
       21.67        20.78        14.93       147.39       117.40        78.71 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-Q1-A5R2 
        0.10         0.89        13.87         0.03         5.42         3.45 
TCGA-UC-A7PF 
       93.99 

$subtype3
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       57.04        11.44        36.56       144.16       177.04       173.29 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A1MQ 
        5.46        19.86        46.32        38.99        40.93        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A7CH 
       73.18        73.45        78.35       100.14        52.01        25.35 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH 
       17.19        60.69        94.95         9.34        13.61        45.83 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A907 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM 
       99.91        23.51         4.47        87.75         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A3HU TCGA-EA-A3QE 
      118.65        28.31        12.36        22.98         2.66         1.18 
TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       14.50         1.81        12.59        45.96         6.64         0.53 
TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN 
        0.07         0.03         0.36         0.10         0.10         0.03 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV 
        6.94         4.47         0.92         0.66         1.58         1.97 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.13         0.07         0.82         5.49         5.85         3.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       19.59         3.88        11.67 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  182.93   147.39   177.04 
subtype1 subtype2 subtype3 
   13.05    13.87    14.50 
[1] "0.1 - 182.9 (13.1)" "0.0 - 147.4 (13.9)" "0.0 - 177.0 (14.5)"
D7V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 37 17     1
  subtype2 35 12     2
  subtype3 36 10     1
D7V3, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          37       35       36
  T2          17       12       10
  T3+T4        1        2        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus        0  1
  subtype1 37 14
  subtype2 32 17
  subtype3 31 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   14
  subtype2   32   17
  subtype3   31   13
   clus
vv  subtype1 subtype2 subtype3
  0       37       32       31
  1       14       17       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 26  3 28
  subtype2 30  0 22
  subtype3 27  1 20
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       26       30       27
  M1        3        0        1
  MX       28       22       20
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             2                               37
  subtype2             0                               60
  subtype3             0                               71
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  16
  subtype2                                   4
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            3
  subtype2                                            1
  subtype3                                            0
D7V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        2        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    37       60       71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 16        4        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         3        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1  7 57
  subtype2 11 54
  subtype3 14 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   57
  subtype2   11   54
  subtype3   14   57
     clus
vv    subtype1 subtype2 subtype3
  NO         7       11       14
  YES       57       54       57
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         9
  subtype2                                1     7                         5
  subtype3                                6     5                         9
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    50
  subtype2                                         0    49
  subtype3                                         1    49
D7V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        6
  ASIAN                                            4        7        5
  BLACK OR AFRICAN AMERICAN                        9        5        9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           50       49       49
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
          cls
clus        0  1
  subtype1  4 47
  subtype2  2 47
  subtype3  7 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   47
  subtype2    2   47
  subtype3    7   50
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        7
  NOT HISPANIC OR LATINO       47       47       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, continuous
D7V13, binary
          cls
clus        0  1
  subtype1 18  6
  subtype2 14  9
  subtype3 19  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    6
  subtype2   14    9
  subtype3   19    7
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       18       14       19
  WITH TUMOR        6        9        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       1      2       3            55       3
  subtype2       0      7       2            50       6
  subtype3       0      2       2            64       3
D7V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  NIGERIA              1        0        0
  RUSSIA               2        7        2
  UKRAINE              3        2        2
  UNITED STATES       55       50       64
  VIETNAM              3        6        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  6 25 29  0  3
  subtype2  7 35 22  1  0
  subtype3  1 34 32  0  2
D7V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        7        1
  G2       25       35       34
  G3       29       22       32
  G4        0        1        0
  GX        3        0        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V16, continuous
D7V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           7
  subtype2                                           9
  subtype3                                           9
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      2
  subtype2                                      4
  subtype3                                      2
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             11
  subtype2                                               2             16
  subtype3                                               1             16
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  34
  subtype2                  27
  subtype3                  28
D7V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            7        9        9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2        4        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                        11       16       16
  LIFELONG NON-SMOKER                                   34       27       28
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V19, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           5       19             2        0        0
  subtype2           5       10             6        1        4
  subtype3           8       15             6        0        4
D7V20, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          5        5        8
  EXTERNAL            19       10       15
  EXTERNAL BEAM        2        6        6
  IMPLANTS             0        1        0
  INTERNAL             0        4        4
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V21, binary
          cls
clus       0 1
  subtype1 5 0
  subtype2 5 1
  subtype3 6 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    5    1
  subtype3    6    3
     clus
vv    subtype1 subtype2 subtype3
  CGY        5        5        6
  GY         0        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
D7V26, continuous
D7V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            1
  subtype2    0    0            0
  subtype3    1    1            0
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                 13
  subtype2                                                 17
  subtype3                                                 11
D7V28, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        0        1
  2010                                                      0        0        1
  COMMON ILIAC                                              1        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)       13       17       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       0
  subtype2                                   3                       5
  subtype3                                   3                       8
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       3
  subtype2                       1                       3
  subtype3                       0                       0
D7V29, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        3
  OTHER LOCATION, SPECIFY                    0        5        8
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    3        3        0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             1
  subtype2                                             1
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              4
  subtype2                                              3
  subtype3                                              3
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                18
  subtype2                                                                                24
  subtype3                                                                                16
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           26
  subtype2                                                                                           24
  subtype3                                                                                           35
D7V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       26
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       24
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       35
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V31, binary
          cls
clus        0  1
  subtype1 19 27
  subtype2 20 23
  subtype3 17 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   27
  subtype2   20   23
  subtype3   17   16
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        19       20       17
  PRESENT       27       23       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V32, continuous
D7V33, continuous
D7V34, binary
          cls
clus        0  1
  subtype1  4 26
  subtype2 20 27
  subtype3 19 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   26
  subtype2   20   27
  subtype3   19   35
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            4       20       19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       26       27       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     3                   46                   2
  subtype2     0                   49                   1
  subtype3     0                   34                   2
D7V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3
  OTHER                       3        0        0
  RADICAL HYSTERECTOMY       46       49       34
  SIMPLE HYSTERECTOMY         2        1        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            4          14         15
  subtype2            2          13         16
  subtype3            2          13         16
D7V37, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        4        2        2
  FORMER USER        14       13       13
  NEVER USED         15       16       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V38, continuous
D7V39, binary
          cls
clus        0  1
  subtype1 29  6
  subtype2 27  8
  subtype3 25  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    6
  subtype2   27    8
  subtype3   25    1
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        29       27       25
  PRESENT        6        8        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V40, binary
          cls
clus        0  1
  subtype1  0  3
  subtype2  2  4
  subtype3  1 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    2    4
  subtype3    1   10
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        2        1
  CISPLATIN          3        4       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V41, continuous
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0    0   6   20   11  2   2    4    5   4   1  0   0  2
  subtype2   1    1   7   19    7  1   3    2    2   4   0  2   0  3
  subtype3   1    0  13   16    6  0   1    1    2   6   1  0   1  3
D7V42, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        1        1
  T1A1        0        1        0
  T1B         6        7       13
  T1B1       20       19       16
  T1B2       11        7        6
  T2          2        1        0
  T2A         2        3        1
  T2A1        4        2        1
  T2A2        5        2        2
  T2B         4        4        6
  T3B         1        0        1
  T4          0        2        0
  TIS         0        0        1
  TX          2        3        3
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V43, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 19  3
  subtype2 31  7
  subtype3 11  6
  subtype4 19 11
  subtype5 25  4
  subtype6 22  4
  subtype7 28  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      22       38       17       30       29       26       31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       3        7        6       11        4        4        3 
$subtype1
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       57.73         0.46        44.22        38.43         0.82        17.85 
TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-DS-A7WH TCGA-EK-A2RL TCGA-EX-A1H6 TCGA-EX-A449 
        9.67         2.73         7.33        23.70         7.92        14.70 
TCGA-EX-A8YF TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LB TCGA-IR-A3LF 
        4.73         2.17         1.35         1.12        66.81        96.95 
TCGA-JW-A69B TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P 
       10.06         3.72         3.72         4.80 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1BM TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MQ TCGA-C5-A2LY 
       57.04        82.85        30.21        53.16        33.90        78.35 
TCGA-C5-A7CG TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XJ TCGA-C5-A8YQ 
      182.93        15.48        85.55        94.95        75.78        23.51 
TCGA-C5-A901 TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A7WI 
       17.03       118.65        28.31       127.36        22.98         8.28 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E 
        1.32         0.82        13.05         1.35        12.66         0.26 
TCGA-EA-A6QX TCGA-EK-A2RB TCGA-EX-A69L TCGA-FU-A23L TCGA-IR-A3LH TCGA-IR-A3LI 
       13.58         0.07         4.47        23.84        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       36.36        16.64         5.42         0.07         3.45         3.39 
TCGA-Q1-A6DW TCGA-RA-A741 
        5.75         3.88 

$subtype3
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        23.67        68.84        36.56       144.16       177.04 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-DR-A0ZL 
       67.46        46.32        38.99         2.43         3.58        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1OA TCGA-EA-A1QT TCGA-EX-A1H5 
       36.76         2.66        28.90        12.36        20.35 

$subtype4
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A2LT 
       11.44        18.74         5.46        35.01        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 
       73.45        52.01        25.35        17.19         9.34        13.61 
TCGA-C5-A8XH TCGA-C5-A8XK TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-EA-A3Y4 TCGA-EA-A43B 
       45.83        99.91       117.99         8.75        14.50         1.81 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 
       45.96         6.64         0.36         0.10         0.03         6.94 
TCGA-FU-A3HY TCGA-JW-A5VG TCGA-JW-A5VL TCGA-LP-A4AX TCGA-MY-A913 TCGA-UC-A7PD 
        0.66        14.43        15.58         0.07         5.49        11.67 

$subtype5
TCGA-C5-A1BL TCGA-C5-A1BQ TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A7UH TCGA-C5-A8XI 
      173.29        19.86        83.05       100.14        60.69         8.35 
TCGA-C5-A902 TCGA-C5-A905 TCGA-DS-A1OC TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A5O9 
        4.90       160.41        12.36         2.66         1.18        13.91 
TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EX-A69M 
       12.59        88.08         0.53         0.03         0.10         6.12 
TCGA-FU-A2QG TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VJ TCGA-JW-A5VK 
        0.92         1.58         1.97        26.56        19.33        20.48 
TCGA-JW-A852 TCGA-LP-A5U3 TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R3 
        5.13         0.82        29.72         4.34         5.85 

$subtype6
TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A3HE TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 
       31.40        35.61        18.02        27.52         6.12         4.47 
TCGA-DS-A7WF TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       16.18         1.35        14.50        12.82        14.89         1.48 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-FU-A23K 
       14.96         0.59         1.18         2.24         0.10         1.22 
TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A57G TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-LP-A4AU 
        1.02         0.82         1.32         4.11       137.16         0.10 
TCGA-PN-A8MA TCGA-Q1-A73R 
        2.96         6.25 

$subtype7
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7XC TCGA-C5-A8ZZ 
       20.42       101.82       134.33        73.41        50.99        20.91 
TCGA-DR-A0ZM TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A5ZD 
       58.88        16.83         0.76         1.74         0.62         0.69 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2RC TCGA-EK-A2RO TCGA-FU-A3NI 
       14.99        13.48         0.36         4.04         0.07         1.45 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.48         3.52        25.41        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI TCGA-R2-A69V 
      147.39       117.40         0.89        13.87         0.03        19.59 
TCGA-UC-A7PF 
       93.99 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.46     0.07     2.43     0.03     0.03     0.10     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   96.95   182.93   177.04   117.99   173.29   137.16   147.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   7.625   20.005   36.760   14.020    8.350    4.290   14.990 
[1] "0.5 - 97.0 (7.6)"   "0.1 - 182.9 (20.0)" "2.4 - 177.0 (36.8)"
[4] "0.0 - 118.0 (14.0)" "0.0 - 173.3 (8.3)"  "0.1 - 137.2 (4.3)" 
[7] "0.0 - 147.4 (15.0)"
D8V2, continuous
          vv
clus       T1 T2 T3+T4
  subtype1 14  5     0
  subtype2 18  9     2
  subtype3 12  2     0
  subtype4 14  3     2
  subtype5 14  8     0
  subtype6 14  7     0
  subtype7 22  5     0
D8V3, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1          14       18       12       14       14       14       22
  T2           5        9        2        3        8        7        5
  T3+T4        0        2        0        2        0        0        0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus        0  1
  subtype1 13  4
  subtype2 19 10
  subtype3  7  7
  subtype4 14  5
  subtype5 13  7
  subtype6 16  4
  subtype7 18  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    4
  subtype2   19   10
  subtype3    7    7
  subtype4   14    5
  subtype5   13    7
  subtype6   16    4
  subtype7   18    7
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       13       19        7       14       13       16       18
  1        4       10        7        5        7        4        7
[1] 2 7
[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       M0 M1 MX
  subtype1  7  1 11
  subtype2 18  1 14
  subtype3  9  0  5
  subtype4 10  1  9
  subtype5  9  0 13
  subtype6 14  1  7
  subtype7 16  0 11
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0        7       18        9       10        9       14       16
  M1        1        1        0        1        0        1        0
  MX       11       14        5        9       13        7       11
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             0                                1
  subtype2             0                               39
  subtype3             0                               17
  subtype4             0                               30
  subtype5             0                               29
  subtype6             2                               19
  subtype7             0                               33
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
  subtype6                                             0
  subtype7                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   1
  subtype3                                   0
  subtype4                                   1
  subtype5                                   0
  subtype6                                   4
  subtype7                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         0
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
  subtype6                                         2
  subtype7                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            4
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
  subtype5                                            0
  subtype6                                            0
  subtype7                                            0
D8V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                     1       39       17
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         4        0        0
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        0        2
  CERVICAL SQUAMOUS CELL CARCINOMA                    30       29       19
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  1        0        4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0        2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0        0
                                               clus
vv                                              subtype7
  ADENOSQUAMOUS                                        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0
[1] 6 7
[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
  subtype1  1 22
  subtype2  9 31
  subtype3  7 10
  subtype4  6 25
  subtype5  3 26
  subtype6  2 25
  subtype7  4 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   22
  subtype2    9   31
  subtype3    7   10
  subtype4    6   25
  subtype5    3   26
  subtype6    2   25
  subtype7    4   29
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         1        9        7        6        3        2        4
  YES       22       31       10       25       26       25       29
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         1
  subtype2                                1     4                         4
  subtype3                                0     2                         3
  subtype4                                3     1                         5
  subtype5                                2     1                         6
  subtype6                                0     3                         2
  subtype7                                1     4                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    21
  subtype2                                         0    30
  subtype3                                         0    12
  subtype4                                         1    21
  subtype5                                         0    20
  subtype6                                         0    21
  subtype7                                         0    23
D8V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        0        3
  ASIAN                                            1        4        2        1
  BLACK OR AFRICAN AMERICAN                        1        4        3        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           21       30       12       21
                                           clus
vv                                          subtype5 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE                 2        0        1
  ASIAN                                            1        3        4
  BLACK OR AFRICAN AMERICAN                        6        2        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0
  WHITE                                           20       21       23
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus        0  1
  subtype1  3 16
  subtype2  1 29
  subtype3  0 14
  subtype4  3 20
  subtype5  4 19
  subtype6  1 22
  subtype7  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   16
  subtype2    1   29
  subtype3    0   14
  subtype4    3   20
  subtype5    4   19
  subtype6    1   22
  subtype7    1   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        1        0        3        4        1
  NOT HISPANIC OR LATINO       16       29       14       20       19       22
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       24
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
D8V13, binary
          cls
clus        0  1
  subtype1  4  1
  subtype2 14  3
  subtype3  8  5
  subtype4  7  5
  subtype5  6  3
  subtype6  4  4
  subtype7  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2   14    3
  subtype3    8    5
  subtype4    7    5
  subtype5    6    3
  subtype6    4    4
  subtype7    8    1
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  TUMOR FREE        4       14        8        7        6        4        8
  WITH TUMOR        1        3        5        5        3        4        1
[1] 2 7
[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       NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1       0      0       0            23       0
  subtype2       0      3       1            33       3
  subtype3       0      1       0            16       0
  subtype4       0      0       2            28       1
  subtype5       0      2       1            25       1
  subtype6       1      2       2            19       3
  subtype7       0      3       1            25       4
D8V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NIGERIA              0        0        0        0        0        1        0
  RUSSIA               0        3        1        0        2        2        3
  UKRAINE              0        1        0        2        1        2        1
  UNITED STATES       23       33       16       28       25       19       25
  VIETNAM              0        3        0        1        1        3        4
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       G1 G2 G3 G4 GX
  subtype1  5 14  3  0  1
  subtype2  1 22 12  1  3
  subtype3  0  8  9  0  0
  subtype4  2  8 19  0  0
  subtype5  2 16 11  0  0
  subtype6  0  8 18  0  1
  subtype7  4 18 11  0  0
D8V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  G1        5        1        0        2        2        0        4
  G2       14       22        8        8       16        8       18
  G3        3       12        9       19       11       18       11
  G4        0        1        0        0        0        0        0
  GX        1        3        0        0        0        1        0
[1] 5 7
[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:" "subtype4"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       4        6        3        2        4        2        6 
 [1] "subtype3" "subtype3" "subtype5" "subtype5" "subtype1" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype7" "subtype2" "subtype5"
[13] "subtype5" "subtype7" "subtype7" "subtype7" "subtype7" "subtype1"
[19] "subtype2" "subtype7" "subtype2" "subtype2" "subtype2"
D8V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           3
  subtype2                                           7
  subtype3                                           3
  subtype4                                           2
  subtype5                                           5
  subtype6                                           2
  subtype7                                           3
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      1
  subtype3                                      2
  subtype4                                      0
  subtype5                                      1
  subtype6                                      0
  subtype7                                      3
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              5
  subtype2                                               1              7
  subtype3                                               0              3
  subtype4                                               1              8
  subtype5                                               0              6
  subtype6                                               0              5
  subtype7                                               1              9
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  12
  subtype2                  22
  subtype3                   8
  subtype4                  11
  subtype5                  10
  subtype6                  14
  subtype7                  12
D8V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3        7        3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        1        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        0
  CURRENT SMOKER                                         5        7        3
  LIFELONG NON-SMOKER                                   12       22        8
                                                 clus
vv                                                subtype4 subtype5 subtype6
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            2        5        2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        1        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        0        0
  CURRENT SMOKER                                         8        6        5
  LIFELONG NON-SMOKER                                   11       10       14
                                                 clus
vv                                                subtype7
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1
  CURRENT SMOKER                                         9
  LIFELONG NON-SMOKER                                   12
[1] 5 7
[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
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           1        7             0        0        0
  subtype2           4       12             5        0        2
  subtype3           6        0             1        1        0
  subtype4           3        6             3        0        2
  subtype5           2        7             1        0        1
  subtype6           2        6             0        0        1
  subtype7           0        6             4        0        2
D8V20, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COMBINATION          1        4        6        3        2        2        0
  EXTERNAL             7       12        0        6        7        6        6
  EXTERNAL BEAM        0        5        1        3        1        0        4
  IMPLANTS             0        0        1        0        0        0        0
  INTERNAL             0        2        0        2        1        1        2
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V21, binary
          cls
clus       0 1
  subtype1 2 0
  subtype2 4 2
  subtype3 0 0
  subtype4 3 1
  subtype5 1 0
  subtype6 3 0
  subtype7 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    0
  subtype2    4    2
  subtype3    0    0
  subtype4    3    1
  subtype5    1    0
  subtype6    3    0
  subtype7    3    1
     clus
vv    subtype1 subtype2 subtype4 subtype5 subtype6 subtype7
  CGY        2        4        3        1        3        3
  GY         0        2        1        0        0        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
D8V26, continuous
D8V27, continuous
          vv
clus       2003 2010 COMMON ILIAC
  subtype1    0    0            0
  subtype2    0    0            0
  subtype3    0    0            0
  subtype4    1    0            0
  subtype5    0    1            0
  subtype6    0    0            1
  subtype7    0    0            0
          vv
clus       PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)
  subtype1                                                  5
  subtype2                                                 13
  subtype3                                                  6
  subtype4                                                  4
  subtype5                                                  6
  subtype6                                                  1
  subtype7                                                  6
D8V28, multiclass
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       5       13        6        5        7        2        6 
 [1] "subtype3" "subtype2" "subtype4" "subtype3" "subtype5" "subtype2"
 [7] "subtype4" "subtype3" "subtype4" "subtype5" "subtype1" "subtype7"
[13] "subtype2" "subtype1" "subtype2" "subtype7" "subtype3" "subtype4"
[19] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype5" "subtype3" "subtype4" "subtype7"
[31] "subtype5" "subtype1" "subtype5" "subtype1" "subtype7" "subtype7"
[37] "subtype2" "subtype2" "subtype2" "subtype5" "subtype2" "subtype7"
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  2003                                                      0        0        0
  2010                                                      0        0        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        5       13        6
                                                    clus
vv                                                   subtype4 subtype5 subtype7
  2003                                                      1        0        0
  2010                                                      0        1        0
  PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR)        4        6        6
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
  subtype6                                   0
  subtype7                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       0
  subtype2                                   3                       4
  subtype3                                   2                       3
  subtype4                                   1                       2
  subtype5                                   1                       2
  subtype6                                   0                       0
  subtype7                                   0                       2
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       1                       2
  subtype3                       0                       1
  subtype4                       0                       1
  subtype5                       0                       1
  subtype6                       0                       0
  subtype7                       0                       0
D8V29, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       2       10        6        4        4        3 
 [1] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2" "subtype5"
 [7] "subtype7" "subtype3" "subtype3" "subtype4" "subtype2" "subtype4"
[13] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[19] "subtype5" "subtype7" "subtype3" "subtype7" "subtype2" "subtype2"
[25] "subtype5" "subtype2" "subtype4"
                                     clus
vv                                    subtype2 subtype3 subtype4 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        3        2        1        1
  OTHER LOCATION, SPECIFY                    4        3        2        2
  POSITIVE BLADDER MARGIN                    1        0        0        0
  POSITIVE VAGINAL MARGIN                    2        1        1        1
                                     clus
vv                                    subtype7
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0
  OTHER LOCATION, SPECIFY                    2
  POSITIVE BLADDER MARGIN                    0
  POSITIVE VAGINAL MARGIN                    0
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             1
  subtype3                                             1
  subtype4                                             0
  subtype5                                             0
  subtype6                                             0
  subtype7                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              0
  subtype2                                              2
  subtype3                                              0
  subtype4                                              1
  subtype5                                              1
  subtype6                                              2
  subtype7                                              4
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                 6
  subtype2                                                                                10
  subtype3                                                                                 8
  subtype4                                                                                 2
  subtype5                                                                                15
  subtype6                                                                                 4
  subtype7                                                                                13
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           13
  subtype2                                                                                           16
  subtype3                                                                                            7
  subtype4                                                                                           16
  subtype5                                                                                            9
  subtype6                                                                                           12
  subtype7                                                                                           12
D8V30, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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)       13
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        7
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype5
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)        9
                                                                                              clus
vv                                                                                             subtype6
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                   4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       12
                                                                                              clus
vv                                                                                             subtype7
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       12
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V31, binary
          cls
clus        0  1
  subtype1 12  5
  subtype2 12 12
  subtype3  4  9
  subtype4  6  8
  subtype5  6  8
  subtype6  6 11
  subtype7 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    5
  subtype2   12   12
  subtype3    4    9
  subtype4    6    8
  subtype5    6    8
  subtype6    6   11
  subtype7   10   13
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  ABSENT        12       12        4        6        6        6       10
  PRESENT        5       12        9        8        8       11       13
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V32, continuous
D8V33, continuous
D8V34, binary
          cls
clus        0  1
  subtype1  0  5
  subtype2  8 19
  subtype3  5  9
  subtype4 12 12
  subtype5  7 16
  subtype6  0 13
  subtype7 11 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    5
  subtype2    8   19
  subtype3    5    9
  subtype4   12   12
  subtype5    7   16
  subtype6    0   13
  subtype7   11   14
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0        8        5       12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA        5       19        9       12
                                          clus
vv                                         subtype5 subtype6 subtype7
  KERATINIZING SQUAMOUS CELL CARCINOMA            7        0       11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       16       13       14
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V35, continuous
          vv
clus       OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  subtype1     2                   14                   1
  subtype2     0                   26                   0
  subtype3     0                   13                   0
  subtype4     0                   13                   2
  subtype5     1                   15                   0
  subtype6     0                   20                   2
  subtype7     0                   28                   0
D8V36, multiclass
                      clus
vv                     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  OTHER                       2        0        0        0        1        0
  RADICAL HYSTERECTOMY       14       26       13       13       15       20
  SIMPLE HYSTERECTOMY         1        0        0        2        0        2
                      clus
vv                     subtype7
  OTHER                       0
  RADICAL HYSTERECTOMY       28
  SIMPLE HYSTERECTOMY         0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            3           7          3
  subtype2            0          10         10
  subtype3            0           1          7
  subtype4            2           6          6
  subtype5            0           4          9
  subtype6            2           6          6
  subtype7            1           6          6
D8V37, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CURRENT USER        3        0        0        2        0        2        1
  FORMER USER         7       10        1        6        4        6        6
  NEVER USED          3       10        7        6        9        6        6
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V38, continuous
D8V39, binary
          cls
clus        0  1
  subtype1 14  1
  subtype2 16  3
  subtype3  9  3
  subtype4 10  1
  subtype5  9  2
  subtype6 10  2
  subtype7 13  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    1
  subtype2   16    3
  subtype3    9    3
  subtype4   10    1
  subtype5    9    2
  subtype6   10    2
  subtype7   13    3
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  ABSENT        14       16        9       10        9       10       13
  PRESENT        1        3        3        1        2        2        3
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V40, binary
          cls
clus       0 1
  subtype1 0 0
  subtype2 1 4
  subtype3 2 3
  subtype4 0 5
  subtype5 0 2
  subtype6 0 1
  subtype7 0 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    0
  subtype2    1    4
  subtype3    2    3
  subtype4    0    5
  subtype5    0    2
  subtype6    0    1
  subtype7    0    2
             clus
vv            subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CARBOPLATIN        1        2        0        0        0        0
  CISPLATIN          4        3        5        2        1        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V41, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 subtype7 
       1        2        3        1        3 
[1] "subtype4" "subtype4" "subtype7" "subtype7" "subtype7" "subtype4"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0    0   1   11    2  0   1    2    1   1   0  0   0  0
  subtype2   0    0   5   10    3  1   1    2    2   3   1  1   0  4
  subtype3   0    0   6    5    1  0   0    0    0   2   0  0   0  0
  subtype4   0    0   6    6    2  0   1    1    1   0   1  1   1  2
  subtype5   1    0   4    3    6  1   0    0    2   5   0  0   0  1
  subtype6   0    0   1    8    5  1   1    1    3   1   0  0   0  1
  subtype7   1    1   3   12    5  0   2    1    0   2   0  0   0  0
D8V42, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1A         0        0        0        0        1        0        1
  T1A1        0        0        0        0        0        0        1
  T1B         1        5        6        6        4        1        3
  T1B1       11       10        5        6        3        8       12
  T1B2        2        3        1        2        6        5        5
  T2          0        1        0        0        1        1        0
  T2A         1        1        0        1        0        1        2
  T2A1        2        2        0        1        0        1        1
  T2A2        1        2        0        1        2        3        0
  T2B         1        3        2        0        5        1        2
  T3B         0        1        0        1        0        0        0
  T4          0        1        0        1        0        0        0
  TIS         0        0        0        1        0        0        0
  TX          0        4        0        2        1        1        0
[1] 14  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V43, continuous
