[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/11541273/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/11589698/CESC-TP.mergedcluster.txt"

nPatients in clinical file=250, in cluster file=307, common to both=250
[1]   8 250
[1] "CN_CNMF"
[1] 3
  1   2   3 
105  57  76 
  1   2   3 
105  57  76 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6 
56 41 44 51 37 14 
 1  2  3  4  5  6 
56 41 44 51 37 14 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
 77 100  62 
  1   2   3 
 77 100  62 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 55 150  34 
  1   2   3 
 55 150  34 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
 79  68 103 
  1   2   3 
 79  68 103 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
48 79 64 20 39 
 1  2  3  4  5 
48 79 64 20 39 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
99 68 72 
 1  2  3 
99 68 72 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 50  42  31 116 
  1   2   3   4 
 50  42  31 116 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDISEASE"                            
 [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_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "POS_LYMPH_NODE_LOCATION"                         
[42] "MENOPAUSE_STATUS"                                
[43] "LYMPHOVASCULAR_INVOLVEMENT"                      
[44] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[45] "LYMPH_NODES_EXAMINED"                            
[46] "KERATINIZATION_SQUAMOUS_CELL"                    
[47] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[48] "HYSTERECTOMY_TYPE"                               
[49] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[50] "HEIGHT_CM_AT_DIAGNOSIS"                          
[51] "FEDPET_OR_CT_RESULTS"                            
[52] "CORPUS_INVOLVEMENT"                              
[53] "CHEMO_CONCURRENT_TYPE"                           
[54] "CERVIX_SUV_RESULTS"                              
[55] "CAUSE_OF_DEATH"                                  
[56] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[57] "AGE_AT_DIAGNOSIS"                                
[58] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 58 rows and 250 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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT 
          NA           NA          109         1031         1345         2226 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        2234         2526         2383           NA         1169           25 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
        1582          548           NA          621         5564         4694 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
          NA           NA           NA          619         4482           NA 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
        2602         1846           NA           NA           NA           83 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        1551           NA          254         2305         3039           NA 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 
          NA          186          636          518          149         4879 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
         136           34         1791         1544         1367         1218 
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          533           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 
         457          456          455          413          410           11 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PG 
         383         1398          799          202         3442           46 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
          NA           NA           13           18           18           44 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
           4          489            2          123            1           11 
TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
          36           NA          721           68            3            2 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
           3            3           NA            1          619          241 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
         211          447          602          186          144           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
         725           28           66           20           31           44 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
          48           45           25          107           41           40 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
          60           34          274          773          217           NA 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
         632          454          287         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-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
         834           NA          747          652          623          474 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
         306          156          204           NA         5957          922 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
         243          343           NA           27            2            9 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
          25            6          422            1          165          904 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
           2          132          167           90          474          406 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
         485          103          491          534          428          483 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
         179          190          316          596          118           NA 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
          NA           NA         1864           NA         1050          883 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 
         615          428           NA           NA         1628           NA 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
        1400          708           NA         1507           NA           NA 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
          NA           NA          707         1365         1295         1280 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        1333         1197         1185          549 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=172,	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=15,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	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=34,	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=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=71,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASMHISTOLOGICGRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 41:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 47:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 49:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 50:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 51:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 52:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 53:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CERVIX_SUV_RESULTS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 56:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 57:'AGE_AT_DIAGNOSIS':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 58:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	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_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CHEMO_CONCURRENT_TYPE"                           
[41] "CERVIX_SUV_RESULTS"                              
[42] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[43] "AGE_AT_DIAGNOSIS"                                
[44] "STAGE_EVENT.CLINICAL_STAGE"                      
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 250 columns, 1 survival variables, and 44 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
127  52   9   4 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
127  52   9   4 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
127  52   9   4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
127  52   9   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=34, 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=71, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=7, binary=FALSE, numeric=FALSE
NEOPLASMHISTOLOGICGRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=19, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=34, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=25, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=34, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=6, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=11, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=48, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=35, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=13, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=15, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=60, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 86 19
  subtype2 38 16
  subtype3 59 15
subtype1 subtype2 subtype3 
     105       54       74 
subtype1 subtype2 subtype3 
      19       16       15 
$subtype1
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-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       46.32        35.01        38.99         0.46         2.43         3.58 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       38.43        18.02        17.85        20.42       182.93       101.82 
TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ 
       17.19        94.95         9.34        75.78         6.12        20.91 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A5RQ 
        1.12        44.94        40.04        58.88       118.65        16.83 
TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       16.18         0.76        13.05         1.18        14.50         1.35 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A6QX TCGA-EK-A2H1 
       12.66        12.82         0.26         1.48        13.58        26.27 
TCGA-EK-A2IP TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A3GJ 
        6.64         1.45         0.07         4.04         0.36         0.10 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K 
        0.10         7.92         6.94        14.70         4.73         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        0.82         3.52         1.32         1.12         9.01        25.41 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       20.78         9.44       147.39       137.16        66.81        96.95 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
       10.06       195.85        30.31        11.28         0.07         0.30 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.87         0.03         5.42         0.07         4.34        15.58 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
       16.14        14.07        15.88         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A8QM 
       11.67        61.28        53.52        46.03        39.78        31.27 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 
       23.24        44.88        43.82 

$subtype2
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MN 
       23.67        11.44         5.46        57.73        35.61        40.93 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UH 
       73.18        73.45        52.01        20.35       147.35        60.69 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KJ 
       50.99        45.83        99.91        27.52         4.47        58.88 
TCGA-DS-A0VM TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
      117.99        17.52         8.28         1.35        14.50         1.81 
TCGA-EA-A556 TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
       14.89        45.96         0.43         0.59         0.59        16.08 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A23L TCGA-FU-A40J TCGA-FU-A5XV 
        1.18         2.24         0.10        23.84         1.35         1.97 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JX-A3PZ TCGA-MY-A913 
        7.13        21.67        78.71        26.56        21.11         5.49 
TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EI 
        2.96         3.39        10.39        12.16        10.03        14.07 
TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A959 TCGA-VS-A9U5 
       19.96        49.55        16.64         4.73        39.35        38.96 

$subtype3
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-A1ML TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
       30.21        53.16        20.91        44.22        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE 
      100.14         0.82       154.32       134.33        15.48        85.55 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KK TCGA-DR-A0ZL 
       13.61         2.73         8.35        23.51        50.76        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       36.76         2.66        22.98        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        0.82         0.62        13.91        15.02        14.99        14.96 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R9 TCGA-EK-A2RD 
       13.48         0.36        12.59         1.51         0.13         0.03 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M 
       23.70         0.07         0.03        20.35        19.79         6.12 
TCGA-FU-A3NI TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LI TCGA-JW-A5VK TCGA-JW-A852 
        1.45        14.93       117.40        81.96        20.48         5.13 
TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MY-A5BD 
        6.71         7.99         0.89         0.82         0.20        29.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-VS-A8EC 
       13.35        15.95        17.56         5.88        93.99        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A954 
       29.03        20.22        32.15        23.28        11.51        42.58 
TCGA-VS-A957 TCGA-WL-A834 
       42.08        18.05 

subtype1 subtype2 subtype3 
    0.03     0.10     0.03 
subtype1 subtype2 subtype3 
  195.85   147.35   173.29 
subtype1 subtype2 subtype3 
  14.500   17.080   17.805 
[1] "0.0 - 195.8 (14.5)" "0.1 - 147.3 (17.1)" "0.0 - 173.3 (17.8)"
D1V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 56 26  2  2
  subtype2 23 14  3  0
  subtype3 42 10  4  0
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       56       23       42
  T2       26       14       10
  T3        2        3        4
  T4        2        0        0
[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"
D1V4, binary
          cls
clus        0  1
  subtype1 58 18
  subtype2 21 13
  subtype3 32 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   18
  subtype2   21   13
  subtype3   32   16
   clus
vv  subtype1 subtype2 subtype3
  0       58       21       32
  1       18       13       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"
          vv
clus       M0 M1 MX
  subtype1 36  4 50
  subtype2 18  3 22
  subtype3 37  1 21
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       36       18       37
  M1        4        3        1
  MX       50       22       21
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               78
  subtype2             2                               49
  subtype3             0                               70
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             3
  subtype2                                             1
  subtype3                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   4
  subtype3                                   4
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         1
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            5
  subtype2                                            0
  subtype3                                            1
D1V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        2        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    78       49       70
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        3        1        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        4        4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        1        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         5        0        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 12 93
  subtype2  8 49
  subtype3 10 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   93
  subtype2    8   49
  subtype3   10   66
     clus
vv    subtype1 subtype2 subtype3
  NO        12        8       10
  YES       93       49       66
[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                                6     7                         9
  subtype2                                0     1                         8
  subtype3                                2    10                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    74
  subtype2                                         0    45
  subtype3                                         0    50
D1V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 6        0        2
  ASIAN                                            7        1       10
  BLACK OR AFRICAN AMERICAN                        9        8        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                           74       45       50
[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  8 67
  subtype2  4 34
  subtype3  4 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   67
  subtype2    4   34
  subtype3    4   48
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        4        4
  NOT HISPANIC OR LATINO       67       34       48
[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 32  9
  subtype2 16  8
  subtype3 23  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32    9
  subtype2   16    8
  subtype3   23    8
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       32       16       23
  WITH TUMOR        9        8        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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      7      3       0      3       4            83       5
  subtype2      8      1       1      2       1            43       1
  subtype3      8      1       0      5       2            52       8
D1V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL               7        8        8
  CANADA               3        1        1
  NIGERIA              0        1        0
  RUSSIA               3        2        5
  UKRAINE              4        1        2
  UNITED STATES       83       43       52
  VIETNAM              5        1        8
[1] 7 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  9 49 40  0  6
  subtype2  2 17 31  1  4
  subtype3  6 40 26  0  4
D1V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        9        2        6
  G2       49       17       40
  G3       40       31       26
  G4        0        1        0
  GX        6        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"
D1V16, continuous
D1V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          13
  subtype2                                           9
  subtype3                                           9
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      3
  subtype2                                      1
  subtype3                                      4
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             24
  subtype2                                               1             11
  subtype3                                               1             17
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  56
  subtype2                  21
  subtype3                  35
D1V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           13        9        9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 3        1        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        1
  CURRENT SMOKER                                        24       11       17
  LIFELONG NON-SMOKER                                   56       21       35
[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
D1V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           7       33             5        4
  subtype2           4       19             4        4
  subtype3           8       23             3        4
D1V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          7        4        8
  EXTERNAL            33       19       23
  EXTERNAL BEAM        5        4        3
  INTERNAL             4        4        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V22, binary
          cls
clus        0  1
  subtype1  9  1
  subtype2  6  2
  subtype3 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2    6    2
  subtype3   10    0
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           9        6       10
  TREATMENT NOT COMPLETED        1        2        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  2                0                  12
  subtype2                  0                2                   9
  subtype3                  0                0                   7
          vv
clus       REGIONAL SITE
  subtype1             3
  subtype2             5
  subtype3             8
D1V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         2        0        0
  LOCAL RECURRENCE           0        2        0
  PRIMARY TUMOR FIELD       12        9        7
  REGIONAL SITE              3        5        8
[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"
D1V24, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2 13  1
  subtype3 10  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   13    1
  subtype3   10    1
     clus
vv    subtype1 subtype2 subtype3
  CGY       11       13       10
  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"
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                      12
  subtype2                                   3                       7
  subtype3                                   2                      10
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       1                       3
  subtype2                       0                       1
  subtype3                       0                       3
D1V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        3        2
  OTHER LOCATION, SPECIFY                   12        7       10
  POSITIVE BLADDER MARGIN                    1        0        0
  POSITIVE VAGINAL MARGIN                    3        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"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             0
  subtype3                                             2
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              4
  subtype2                                              2
  subtype3                                             10
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                29
  subtype2                                                                                12
  subtype3                                                                                27
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           53
  subtype2                                                                                           27
  subtype3                                                                                           25
D1V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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)                  29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       53
                                                                                              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)                  12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       25
[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"
D1V33, binary
          cls
clus        0  1
  subtype1 37 30
  subtype2  9 18
  subtype3 22 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   30
  subtype2    9   18
  subtype3   22   22
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        37        9       22
  PRESENT       30       18       22
[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"
D1V34, continuous
D1V35, continuous
D1V36, binary
          cls
clus        0  1
  subtype1 19 42
  subtype2  8 21
  subtype3 16 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   42
  subtype2    8   21
  subtype3   16   31
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA           19        8       16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       42       21       31
[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"
D1V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          23         23
  subtype2            3          12         11
  subtype3            2          14         23
D1V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        5        3        2
  FORMER USER        23       12       14
  NEVER USED         23       11       23
[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"
D1V39, continuous
D1V40, binary
          cls
clus        0  1
  subtype1 44  6
  subtype2 14  5
  subtype3 31  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    6
  subtype2   14    5
  subtype3   31    5
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        44       14       31
  PRESENT        6        5        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           1         4     1
  subtype2           0         7     0
  subtype3           0         4     0
D1V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        1        0        0
  CISPLATIN          4        7        4
  OTHER              1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V42, continuous
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    1  13   29   13  2   5    3    7   9  1   1  2   0  6
  subtype2   0    0   7   13    3  0   0    4    2   8  0   3  0   1  2
  subtype3   1    0  10   23    8  2   3    0    0   5  0   4  0   0  6
D1V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        0        1
  T1A1        1        0        0
  T1B        13        7       10
  T1B1       29       13       23
  T1B2       13        3        8
  T2          2        0        2
  T2A         5        0        3
  T2A1        3        4        0
  T2A2        7        2        0
  T2B         9        8        5
  T3          1        0        0
  T3B         1        3        4
  T4          2        0        0
  TIS         0        1        0
  TX          6        2        6
[1] 15  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         1         0       12        35        15
  subtype2       1        0         0         1        7        13         7
  subtype3       2        2         0         0       12        21        10
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         4          2          5         9         1
  subtype2        0         2          3          2        12         0
  subtype3        3         0          0          0         6         0
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1         14         1         5
  subtype2          8         0         0
  subtype3         12         2         2
D1V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        2
  STAGE IA          0        0        2
  STAGE IA1         1        0        0
  STAGE IA2         0        1        0
  STAGE IB         12        7       12
  STAGE IB1        35       13       21
  STAGE IB2        15        7       10
  STAGE II          0        0        3
  STAGE IIA         4        2        0
  STAGE IIA1        2        3        0
  STAGE IIA2        5        2        0
  STAGE IIB         9       12        6
  STAGE III         1        0        0
  STAGE IIIB       14        8       12
  STAGE IVA         1        0        2
  STAGE IVB         5        0        2
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 43 12
  subtype2 35  6
  subtype3 34 10
  subtype4 30 19
  subtype5 30  5
  subtype6 13  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      55       41       44       49       35       14 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12        6       10       19        5        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        20.35         2.73 
TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH 
        6.12         1.12        58.88        50.76        16.18        17.52 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2R7 
        1.35        14.50        12.82        14.89        14.96         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 
        1.45        23.70         2.24         0.10         7.92        14.70 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G 
        4.73         1.22         2.17         1.02         1.35         1.32 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI 
        1.12         9.44       137.16        66.81        96.95        81.96 
TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 
        3.29        10.06        30.31        29.72         2.96        15.58 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73S TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH 
       16.14        15.88        10.39        19.96        23.28        39.78 
TCGA-VS-A952 
       44.88 

$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       147.35        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-A2RA 
       12.66         1.48        13.58         6.64         1.51        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV 
        0.07         4.04         0.92         0.66         1.58         1.97 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
      147.39       117.40        26.56        20.48        15.58         5.13 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-Q1-A5R2 TCGA-Q1-A73R 
        6.71       195.85         0.82         0.20        13.35         6.25 
TCGA-VS-A8EK TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A954 TCGA-WL-A834 
       27.25        11.51        49.55        42.58        18.05 

$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-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        50.99        40.04        87.75        58.88 
TCGA-DS-A1O9 TCGA-DS-A1OD TCGA-EA-A1QS TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE 
        8.75       127.36         0.76         2.66        13.05         1.18 
TCGA-EA-A5ZD TCGA-EA-A78R TCGA-EK-A2H1 TCGA-EK-A2RD TCGA-EK-A2RN TCGA-EX-A3L1 
       15.02        13.48        26.27         0.03         0.10         6.94 
TCGA-EX-A69L TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AU 
       19.79         3.52        21.67        14.93        36.36        11.28 
TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MY-A5BE TCGA-Q1-A73O TCGA-R2-A69V TCGA-VS-A8EI 
        0.89        13.87         0.07        14.07        19.59        14.07 
TCGA-VS-A8QM TCGA-VS-A94Z 
       31.27        23.24 

$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       154.32        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-A2PL TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.26        13.91        45.96         0.43         0.36         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-GH-A9DA TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VI 
        0.10         0.03         9.01        78.71        27.42        24.56 
TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-Q1-A6DT TCGA-UC-A7PD 
       21.44        21.11         0.07         5.49         3.39        11.67 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A94X 
       10.03        20.22        53.52        32.15        46.03        16.64 
TCGA-VS-A94Y 
        4.73 

$subtype5
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1M8 TCGA-C5-A1ML TCGA-C5-A3HL TCGA-C5-A7CK 
       23.67        68.84        30.21        20.91        20.42       134.33 
TCGA-C5-A7UE TCGA-C5-A8XJ TCGA-C5-A8ZZ TCGA-DG-A2KL TCGA-DS-A0VK TCGA-DS-A1OB 
       85.55        75.78        20.91        44.94        36.76        28.31 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 
       22.98        16.83         1.32         0.82         0.62         1.35 
TCGA-EA-A97N TCGA-EK-A2IR TCGA-EK-A2PM TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A23L 
        0.36       113.16         0.59         0.07        20.35        23.84 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-HG-A2PA TCGA-JX-A5QV TCGA-MU-A5YI TCGA-MU-A8JM 
        1.48         0.82        25.41         7.99         0.03         5.42 
TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG 
       17.56         5.88        93.99        34.52        29.03 

$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-EK-A2R9 TCGA-EX-A69M TCGA-FU-A3NI TCGA-HM-A3JK TCGA-LP-A5U2 TCGA-MY-A5BF 
        0.13         6.12         1.45        20.78         0.30         4.34 
TCGA-Q1-A5R3 TCGA-RA-A741 
       15.95         3.88 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.07     0.03     0.03     0.03     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  137.16   195.85   182.93   154.32   134.33    53.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   14.96    15.58    19.69    17.19    20.91     5.51 
[1] "0.1 - 137.2 (15.0)" "0.1 - 195.8 (15.6)" "0.0 - 182.9 (19.7)"
[4] "0.0 - 154.3 (17.2)" "0.0 - 134.3 (20.9)" "0.1 - 53.2 (5.5)"  
D2V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 33 13  1  1
  subtype2 20  7  2  1
  subtype3 24 10  1  1
  subtype4 21 10  2  1
  subtype5 20  5  2  0
  subtype6  7  3  0  0
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       33       20       24       21       20        7
  T2       13        7       10       10        5        3
  T3        1        2        1        2        2        0
  T4        1        1        1        1        0        0
[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"
D2V4, binary
          cls
clus        0  1
  subtype1 30 13
  subtype2 15 12
  subtype3 22 11
  subtype4 23  5
  subtype5 18  6
  subtype6  7  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   13
  subtype2   15   12
  subtype3   22   11
  subtype4   23    5
  subtype5   18    6
  subtype6    7    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       30       15       22       23       18        7
  1       13       12       11        5        6        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"
          vv
clus       M0 M1 MX
  subtype1 23  5 21
  subtype2 17  0 16
  subtype3 21  1 16
  subtype4 19  2 16
  subtype5 16  0 13
  subtype6  3  0  7
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       23       17       21       19       16        3
  M1        5        0        1        2        0        0
  MX       21       16       16       16       13        7
[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             4                               20
  subtype2             0                               39
  subtype3             0                               44
  subtype4             0                               51
  subtype5             0                               37
  subtype6             0                               13
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
  subtype6                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  20
  subtype2                                   2
  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                                            6
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
  subtype5                                            0
  subtype6                                            0
D2V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    20       39       44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20        2        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         6        0        0
                                               clus
vv                                              subtype4 subtype5 subtype6
  ADENOSQUAMOUS                                        0        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    51       37       13
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0        1
  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 52
  subtype2  3 38
  subtype3  8 36
  subtype4 11 40
  subtype5  7 30
  subtype6  2 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   52
  subtype2    3   38
  subtype3    8   36
  subtype4   11   40
  subtype5    7   30
  subtype6    2   12
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         4        3        8       11        7        2
  YES       52       38       36       40       30       12
[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                                1     4                         3
  subtype2                                1     4                         4
  subtype3                                1     6                         6
  subtype4                                4     3                         8
  subtype5                                1     0                         2
  subtype6                                0     2                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    43
  subtype2                                         0    29
  subtype3                                         0    28
  subtype4                                         1    34
  subtype5                                         0    29
  subtype6                                         0     9
D2V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        1        4
  ASIAN                                            4        4        6        3
  BLACK OR AFRICAN AMERICAN                        3        4        6        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           43       29       28       34
                                           clus
vv                                          subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0
  ASIAN                                            0        2
  BLACK OR AFRICAN AMERICAN                        2        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0
  WHITE                                           29        9
[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  6 35
  subtype2  4 25
  subtype3  1 33
  subtype4  5 29
  subtype5  1 22
  subtype6  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   35
  subtype2    4   25
  subtype3    1   33
  subtype4    5   29
  subtype5    1   22
  subtype6    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        4        1        5        1        0
  NOT HISPANIC OR LATINO       35       25       33       29       22       11
[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 18  7
  subtype2 10  5
  subtype3 18  4
  subtype4 15  8
  subtype5  9  3
  subtype6  5  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    7
  subtype2   10    5
  subtype3   18    4
  subtype4   15    8
  subtype5    9    3
  subtype6    5    1
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  TUMOR FREE       18       10       18       15        9        5
  WITH TUMOR        7        5        4        8        3        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"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      4      3       1      2       1            43       2
  subtype2      4      0       0      2       2            30       3
  subtype3      3      1       0      3       0            33       4
  subtype4      7      0       0      0       3            38       3
  subtype5      2      1       0      4       1            29       0
  subtype6      0      0       0      0       0            12       2
D2V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  BRAZIL               4        4        3        7        2        0
  CANADA               3        0        1        0        1        0
  NIGERIA              1        0        0        0        0        0
  RUSSIA               2        2        3        0        4        0
  UKRAINE              1        2        0        3        1        0
  UNITED STATES       43       30       33       38       29       12
  VIETNAM              2        3        4        3        0        2
[1] 7 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 24 23  0  3
  subtype2  1 21 18  0  1
  subtype3  2 22 17  0  3
  subtype4  1 22 22  1  3
  subtype5  4 18 11  0  3
  subtype6  1  5  7  0  1
D2V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  G1        6        1        2        1        4        1
  G2       24       21       22       22       18        5
  G3       23       18       17       22       11        7
  G4        0        0        0        1        0        0
  GX        3        1        3        3        3        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                                           6
  subtype2                                           7
  subtype3                                           6
  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              8
  subtype3                                               0              9
  subtype4                                               1             14
  subtype5                                               1              9
  subtype6                                               0              3
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  31
  subtype2                  18
  subtype3                  22
  subtype4                  21
  subtype5                  11
  subtype6                   5
D2V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            6        7        6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        0
  CURRENT SMOKER                                        10        8        9
  LIFELONG NON-SMOKER                                   31       18       22
                                                 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                                        14        9        3
  LIFELONG NON-SMOKER                                   21       11        5
[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
D2V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       20             1        0        1
  subtype2           3       11             0        1        2
  subtype3           5       13             3        0        0
  subtype4           6       16             5        0        4
  subtype5           2        8             5        0        4
  subtype6           1        4             1        0        0
D2V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMBINATION          3        3        5        6        2        1
  EXTERNAL            20       11       13       16        8        4
  EXTERNAL BEAM        1        0        3        5        5        1
  IMPLANTS             0        1        0        0        0        0
  INTERNAL             1        2        0        4        4        0
[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"
D2V22, binary
          cls
clus       0 1
  subtype1 4 0
  subtype2 2 0
  subtype3 7 1
  subtype4 8 2
  subtype5 7 0
  subtype6 1 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2    2    0
  subtype3    7    1
  subtype4    8    2
  subtype5    7    0
  subtype6    1    0
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COMPLETED AS PLANNED           4        2        7        8        7        1
  TREATMENT NOT COMPLETED        0        0        1        2        0        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       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   3
  subtype2                  0                0                   1
  subtype3                  0                1                   7
  subtype4                  1                1                   9
  subtype5                  0                0                   7
  subtype6                  0                0                   1
          vv
clus       REGIONAL SITE
  subtype1             1
  subtype2             5
  subtype3             0
  subtype4             4
  subtype5             3
  subtype6             0
D2V23, multiclass
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5        6        8       15       10        1 
 [1] "subtype4" "subtype4" "subtype3" "subtype2" "subtype5" "subtype4"
 [7] "subtype1" "subtype2" "subtype5" "subtype2" "subtype3" "subtype4"
[13] "subtype5" "subtype4" "subtype4" "subtype1" "subtype5" "subtype4"
[19] "subtype5" "subtype5" "subtype1" "subtype3" "subtype5" "subtype3"
[25] "subtype3" "subtype1" "subtype4" "subtype4" "subtype5" "subtype4"
[31] "subtype3" "subtype5" "subtype5" "subtype4" "subtype3" "subtype4"
[37] "subtype4" "subtype4" "subtype2" "subtype2" "subtype1" "subtype4"
[43] "subtype3" "subtype2"
                     clus
vv                    subtype1 subtype2 subtype3 subtype4 subtype5
  DISTANT RECURRENCE         1        0        0        1        0
  LOCAL RECURRENCE           0        0        1        1        0
  PRIMARY TUMOR FIELD        3        1        7        9        7
  REGIONAL SITE              1        5        0        4        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2  4  0
  subtype3  5  1
  subtype4 10  2
  subtype5  6  0
  subtype6  1  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    4    0
  subtype3    5    1
  subtype4   10    2
  subtype5    6    0
  subtype6    1    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CGY        5        4        5       10        6        1
  GY         0        0        1        2        0        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"
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, continuous
          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                       7
  subtype2                                   1                       3
  subtype3                                   0                       8
  subtype4                                   2                       7
  subtype5                                   3                       5
  subtype6                                   0                       3
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       0                       2
  subtype3                       0                       2
  subtype4                       1                       1
  subtype5                       0                       2
  subtype6                       0                       0
D2V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0        2
  OTHER LOCATION, SPECIFY                    7        3        8        7
  POSITIVE BLADDER MARGIN                    0        0        0        1
  POSITIVE VAGINAL MARGIN                    2        2        2        1
                                     clus
vv                                    subtype5 subtype6
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        3        0
  OTHER LOCATION, SPECIFY                    5        3
  POSITIVE BLADDER MARGIN                    0        0
  POSITIVE VAGINAL MARGIN                    2        0
[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       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                                              4
  subtype2                                              3
  subtype3                                              3
  subtype4                                              2
  subtype5                                              2
  subtype6                                              1
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                14
  subtype2                                                                                15
  subtype3                                                                                14
  subtype4                                                                                 4
  subtype5                                                                                15
  subtype6                                                                                 6
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           29
  subtype2                                                                                           14
  subtype3                                                                                           20
  subtype4                                                                                           26
  subtype5                                                                                           11
  subtype6                                                                                            5
D2V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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
                                                                                              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)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       14
                                                                                              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)       20
                                                                                              clus
vv                                                                                             subtype4
  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)       26
                                                                                              clus
vv                                                                                             subtype5
  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)                  15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       11
                                                                                              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)        5
[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"
D2V33, binary
          cls
clus        0  1
  subtype1 20 20
  subtype2  8 14
  subtype3 13 13
  subtype4 12  9
  subtype5 13 12
  subtype6  2  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   20
  subtype2    8   14
  subtype3   13   13
  subtype4   12    9
  subtype5   13   12
  subtype6    2    6
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        20        8       13       12       13        2
  PRESENT       20       14       13        9       12        6
[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"
D2V34, continuous
D2V35, continuous
D2V36, binary
          cls
clus        0  1
  subtype1  1 15
  subtype2  6 21
  subtype3 10 22
  subtype4 15 18
  subtype5 15 13
  subtype6  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   15
  subtype2    6   21
  subtype3   10   22
  subtype4   15   18
  subtype5   15   13
  subtype6    2    7
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            1        6       10       15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       15       21       22       18
                                          clus
vv                                         subtype5 subtype6
  KERATINIZING SQUAMOUS CELL CARCINOMA           15        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"
D2V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          15         11
  subtype2            1           8         11
  subtype3            1           7         12
  subtype4            2          10         10
  subtype5            1           4         10
  subtype6            0           3          4
D2V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CURRENT USER        5        1        1        2        1        0
  FORMER USER        15        8        7       10        4        3
  NEVER USED         11       11       12       10       10        4
[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"
D2V39, continuous
D2V40, binary
          cls
clus        0  1
  subtype1 29  5
  subtype2 15  2
  subtype3 15  4
  subtype4 15  1
  subtype5 16  5
  subtype6  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    5
  subtype2   15    2
  subtype3   15    4
  subtype4   15    1
  subtype5   16    5
  subtype6    5    0
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ABSENT        29       15       15       15       16        5
  PRESENT        5        2        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         2     0
  subtype2           1         1     0
  subtype3           1         5     1
  subtype4           0         8     0
  subtype5           1         2     0
  subtype6           0         0     0
D2V41, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        2        7        8        3 
 [1] "subtype5" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype5"
[13] "subtype4" "subtype3" "subtype5" "subtype4" "subtype3" "subtype3"
             clus
vv            subtype3 subtype4 subtype5
  CARBOPLATIN        1        0        1
  CISPLATIN          5        8        2
  OTHER              1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V42, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        1        3        4        3        1 
 [1] "subtype4" "subtype3" "subtype5" "subtype4" "subtype3" "subtype5"
 [7] "subtype4" "subtype3" "subtype5" "subtype4"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    0   3   23    7  0   2    3    3   5  0   1  1   0  1
  subtype2   1    0   4   10    5  2   1    0    2   2  1   1  1   0  5
  subtype3   0    0   8   14    2  2   1    2    1   4  0   1  1   0  2
  subtype4   0    0  11    7    3  0   1    1    2   6  0   2  1   1  4
  subtype5   0    1   6    8    5  0   2    1    1   1  0   2  0   0  2
  subtype6   0    0   0    4    3  0   1    0    1   1  0   0  0   0  1
D2V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1A         0        1        0        0        0        0
  T1A1        0        0        0        0        1        0
  T1B         3        4        8       11        6        0
  T1B1       23       10       14        7        8        4
  T1B2        7        5        2        3        5        3
  T2          0        2        2        0        0        0
  T2A         2        1        1        1        2        1
  T2A1        3        0        2        1        1        0
  T2A2        3        2        1        2        1        1
  T2B         5        2        4        6        1        1
  T3          0        1        0        0        0        0
  T3B         1        1        1        2        2        0
  T4          1        1        1        1        0        0
  TIS         0        0        0        1        0        0
  TX          1        5        2        4        2        1
[1] 15  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       0        0         0         0        3        25        10
  subtype2       1        1         0         0        6         8         5
  subtype3       0        1         0         0        7        14         3
  subtype4       1        0         0         0       13         9         5
  subtype5       2        0         1         1        5         9         7
  subtype6       0        0         0         0        1         3         4
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        0         1          1          2         5         0
  subtype2        2         0          0          1         2         1
  subtype3        1         1          2          0         3         0
  subtype4        0         4          1          1         8         0
  subtype5        1         1          1          1         4         0
  subtype6        0         0          0          2         1         0
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1          5         0         4
  subtype2          7         2         1
  subtype3         10         1         1
  subtype4          6         1         1
  subtype5          3         1         0
  subtype6          2         0         0
D2V45, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        1        0        1        2        0
  STAGE IA          0        1        1        0        0        0
  STAGE IA1         0        0        0        0        1        0
  STAGE IA2         0        0        0        0        1        0
  STAGE IB          3        6        7       13        5        1
  STAGE IB1        25        8       14        9        9        3
  STAGE IB2        10        5        3        5        7        4
  STAGE II          0        2        1        0        1        0
  STAGE IIA         1        0        1        4        1        0
  STAGE IIA1        1        0        2        1        1        0
  STAGE IIA2        2        1        0        1        1        2
  STAGE IIB         5        2        3        8        4        1
  STAGE III         0        1        0        0        0        0
  STAGE IIIB        5        7       10        6        3        2
  STAGE IVA         0        2        1        1        1        0
  STAGE IVB         4        1        1        1        0        0
[1] 16  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 61 14
  subtype2 80 18
  subtype3 42 19
subtype1 subtype2 subtype3 
      75       98       61 
subtype1 subtype2 subtype3 
      14       18       19 
$subtype1
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-A1ML TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 
        0.46        20.91        44.22        83.05        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ 
       18.02        17.85        20.35         2.73        50.99        75.78 
TCGA-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A1OD TCGA-DS-A7WF 
        6.12         1.12        58.88        50.76       127.36        16.18 
TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       17.52         1.35         1.35        14.50        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RL 
        1.48        14.99        14.96         0.59         0.13        23.70 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF 
        2.24         0.10         7.92        14.70         6.12         4.73 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A40J TCGA-FU-A57G 
        1.22         2.17         1.02         1.48         1.35         1.32 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.12        25.41         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B TCGA-JX-A3Q8 
      117.40        96.95        81.96         3.29        10.06        30.31 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 
        0.30         0.20        29.72         0.07         2.96        15.58 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-VS-A8EJ 
       16.14        15.88         6.25        10.39         3.88        19.96 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       23.28        39.78        44.88 

$subtype2
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-C5-A8XI TCGA-C5-A8YQ 
      134.33        15.48       147.35        85.55         8.35        23.51 
TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A905 TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        17.03       160.41        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A1QT 
       58.88        36.76         2.66        22.98        16.83        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD 
        1.74         1.32         0.82         0.62         2.66        13.05 
TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX 
        1.18        12.66         0.26        13.91        15.02        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RA 
       13.48         0.36       113.16         1.51         0.59        16.08 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A23L 
        0.07         4.04         0.10         0.07        20.35        23.84 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         0.66         1.45         1.58         0.82         3.52 
TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-JW-A5VJ 
        1.97        21.67        20.78        14.93        36.36        21.44 
TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW 
       20.48         5.13         6.71       195.85         7.99         0.89 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R2 
        0.82        13.87         0.03         5.42         4.34        13.35 
TCGA-Q1-A6DW TCGA-Q1-A73Q TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       17.56         5.88        93.99        34.52        29.03        20.22 
TCGA-VS-A8EK TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Z 
       27.25        32.15        11.51        49.55        31.27        23.24 
TCGA-VS-A954 TCGA-WL-A834 
       42.58        18.05 

$subtype3
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-A2LY TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UH 
       73.45        78.35        52.01       154.32        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YR 
       94.95         9.34        13.61        45.83        99.91        27.52 
TCGA-C5-A902 TCGA-C5-A907 TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC 
        4.90         4.47       117.99       118.65        28.31        12.36 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H0 
        8.28         0.76        14.50         1.81        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RE TCGA-EK-A2RJ 
       26.27         6.64         0.43         1.45         0.36         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-GH-A9DA TCGA-IR-A3LH 
        0.10         0.03         6.94        19.79         9.01        78.71 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU 
       26.56        27.42        24.56        15.58        21.11        11.28 
TCGA-LP-A4AX TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V 
        0.07         5.49        15.95         3.39        14.07        19.59 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A94X 
       11.67        10.03        14.07        53.52        46.03        16.64 
TCGA-VS-A94Y 
        4.73 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  147.39   195.85   154.32 
subtype1 subtype2 subtype3 
  14.990   17.295   15.580 
[1] "0.1 - 147.4 (15.0)" "0.0 - 195.8 (17.3)" "0.0 - 154.3 (15.6)"
D3V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 46 16  1  1
  subtype2 48 21  5  2
  subtype3 29 10  2  0
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       46       48       29
  T2       16       21       10
  T3        1        5        2
  T4        1        2        0
[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"
D3V4, binary
          cls
clus        0  1
  subtype1 45 14
  subtype2 40 27
  subtype3 27  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   14
  subtype2   40   27
  subtype3   27    8
   clus
vv  subtype1 subtype2 subtype3
  0       45       40       27
  1       14       27        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       M0 M1 MX
  subtype1 35  5 25
  subtype2 37  1 43
  subtype3 24  2 20
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       35       37       24
  M1        5        1        2
  MX       25       43       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             4                               38
  subtype2             0                              100
  subtype3             0                               62
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             5
  subtype2                                             0
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  22
  subtype2                                   0
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            6
  subtype2                                            0
  subtype3                                            0
D3V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    38      100       62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        5        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 22        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         6        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"
D3V7, binary
          cls
clus        0  1
  subtype1  8 69
  subtype2 14 86
  subtype3 11 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   69
  subtype2   14   86
  subtype3   11   51
     clus
vv    subtype1 subtype2 subtype3
  NO         8       14       11
  YES       69       86       51
[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                                1     7                         4
  subtype2                                2     7                        11
  subtype3                                4     4                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    59
  subtype2                                         0    70
  subtype3                                         1    41
D3V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        2        4
  ASIAN                                            7        7        4
  BLACK OR AFRICAN AMERICAN                        4       11       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           59       70       41
[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  6 50
  subtype2  5 63
  subtype3  6 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   50
  subtype2    5   63
  subtype3    6   38
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        5        6
  NOT HISPANIC OR LATINO       50       63       38
[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 26  8
  subtype2 29  9
  subtype3 19  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    8
  subtype2   29    9
  subtype3   19    9
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       26       29       19
  WITH TUMOR        8        9        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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      4      3       1      3       2            59       5
  subtype2     10      2       0      7       3            72       6
  subtype3      6      0       0      1       2            50       3
D3V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL               4       10        6
  CANADA               3        2        0
  NIGERIA              1        0        0
  RUSSIA               3        7        1
  UKRAINE              2        3        2
  UNITED STATES       59       72       50
  VIETNAM              5        6        3
[1] 7 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 35  0  5
  subtype2  7 60 29  0  4
  subtype3  2 20 32  1  5
D3V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        7        2
  G2       30       60       20
  G3       35       29       32
  G4        0        0        1
  GX        5        4        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"
D3V16, continuous
D3V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          12
  subtype2                                          16
  subtype3                                           5
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      7
  subtype3                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             14
  subtype2                                               2             25
  subtype3                                               1             13
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  40
  subtype2                  37
  subtype3                  29
D3V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           12       16        5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        7        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                        14       25       13
  LIFELONG NON-SMOKER                                   40       37       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
D3V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           6       24             2        1
  subtype2           8       27             7        6
  subtype3           5       21             6        4
D3V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          6        8        5
  EXTERNAL            24       27       21
  EXTERNAL BEAM        2        7        6
  INTERNAL             1        6        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V22, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2 12  1
  subtype3  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2   12    1
  subtype3    8    2
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           8       12        8
  TREATMENT NOT COMPLETED        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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   4
  subtype2                  0                1                  10
  subtype3                  1                1                  14
          vv
clus       REGIONAL SITE
  subtype1             1
  subtype2            10
  subtype3             2
D3V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        4       10       14
  REGIONAL SITE              1       10        2
[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"
D3V24, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 15  1
  subtype3 11  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   15    1
  subtype3   11    2
     clus
vv    subtype1 subtype2 subtype3
  CGY        5       15       11
  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"
D3V25, continuous
D3V26, continuous
D3V27, continuous
D3V28, continuous
D3V29, continuous
D3V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                      10
  subtype2                                   2                      13
  subtype3                                   2                       9
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       3
  subtype2                       1                       4
  subtype3                       0                       1
D3V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        2
  OTHER LOCATION, SPECIFY                   10       13        9
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    3        4        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                                             0
  subtype2                                             2
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              5
  subtype2                                              8
  subtype3                                              2
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                22
  subtype2                                                                                36
  subtype3                                                                                 7
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           36
  subtype2                                                                                           37
  subtype3                                                                                           32
D3V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       36
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              clus
vv                                                                                             subtype3
  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)                   7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       32
[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"
D3V33, binary
          cls
clus        0  1
  subtype1 25 29
  subtype2 27 32
  subtype3 15 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   29
  subtype2   27   32
  subtype3   15   10
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        25       27       15
  PRESENT       29       32       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V34, continuous
D3V35, continuous
D3V36, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2 28 44
  subtype3 16 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2   28   44
  subtype3   16   27
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            4       28       16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       23       44       27
[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"
D3V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            6          20         15
  subtype2            1          16         28
  subtype3            3          11         13
D3V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        6        1        3
  FORMER USER        20       16       11
  NEVER USED         15       28       13
[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"
D3V39, continuous
D3V40, binary
          cls
clus        0  1
  subtype1 39  7
  subtype2 33  9
  subtype3 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    7
  subtype2   33    9
  subtype3   21    0
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        39       33       21
  PRESENT        7        9        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         4     0
  subtype2           1         6     0
  subtype3           1         7     1
D3V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        1
  CISPLATIN          4        6        7
  OTHER              0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        7        4 
 [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    0   4   32   10  2   3    3    3   5  0   1  1   0  2
  subtype2   1    1  17   20    9  1   4    2    5   9  1   4  2   0  7
  subtype3   0    0  11   12    6  1   1    2    2   4  0   2  0   1  6
D3V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        1        0
  T1A1        0        1        0
  T1B         4       17       11
  T1B1       32       20       12
  T1B2       10        9        6
  T2          2        1        1
  T2A         3        4        1
  T2A1        3        2        2
  T2A2        3        5        2
  T2B         5        9        4
  T3          0        1        0
  T3B         1        4        2
  T4          1        2        0
  TIS         0        0        1
  TX          2        7        6
[1] 15  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        4        37        14
  subtype2       2        2         1         1       15        19        10
  subtype3       1        0         0         0       15        11        10
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         1          1          2         6         0
  subtype2        3         2          2          4         9         1
  subtype3        0         3          2          1         8         0
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1          6         0         4
  subtype2         19         4         2
  subtype3          8         0         1
D3V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        2        1
  STAGE IA          0        2        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          4       15       15
  STAGE IB1        37       19       11
  STAGE IB2        14       10       10
  STAGE II          1        3        0
  STAGE IIA         1        2        3
  STAGE IIA1        1        2        2
  STAGE IIA2        2        4        1
  STAGE IIB         6        9        8
  STAGE III         0        1        0
  STAGE IIIB        6       19        8
  STAGE IVA         0        4        0
  STAGE IVB         4        2        1
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1  43  11
  subtype2 119  28
  subtype3  21  12
subtype1 subtype2 subtype3 
      54      147       33 
subtype1 subtype2 subtype3 
      11       28       12 
$subtype1
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-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT 
       44.22        38.43         0.82        20.35         2.73         6.12 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 
        1.12        58.88        50.76        16.18        17.52         1.35 
TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2R7 
       14.50        12.82        14.89         1.48        14.96         0.59 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23K 
       23.70         2.24         0.10         7.92        14.70         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 
        2.17         1.02         1.35         1.32         1.12         9.44 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B 
      137.16        66.81        96.95        81.96         3.29        10.06 
TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV 
       30.31         0.20        29.72         2.96        15.58        16.14 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       15.88         6.25        19.96        23.28        39.78        44.88 

$subtype2
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        23.67        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       30.21        38.99         2.43        20.91        40.93         3.58 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       83.05        78.35       100.14        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE 
      154.32       101.82       134.33        15.48       147.35        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       60.69        94.95        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-C5-A905 TCGA-DG-A2KL 
       75.78        23.51        20.91        17.03       160.41        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A5RQ 
      118.65        28.31        12.36       127.36        22.98        16.83 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E 
        2.66        13.05         1.18         1.35        12.66         0.26 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       13.91        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PL 
       12.59        45.96         6.64       113.16         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        0.59         0.13        16.08         0.07         4.04         0.36 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M 
        0.10         0.07         0.10        20.35        19.79         6.12 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       23.84         0.92         0.66         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.82         3.52         1.97        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI 
       14.93       147.39       117.40        26.56        36.36        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       21.44        20.48        15.58         5.13         6.71       195.85 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
        7.99        11.28         0.89         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.03         5.42         0.07         4.34        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V 
        3.39        17.56        14.07         5.88        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
        3.88        93.99        34.52        29.03        20.22        14.07 
TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       27.25        53.52        32.15        11.51        49.55        31.27 
TCGA-VS-A94Z TCGA-VS-A954 TCGA-WL-A834 
       23.24        42.58        18.05 

$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-A3HE TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A902 
       18.02        17.19         9.34        99.91        27.52         4.90 
TCGA-C5-A907 TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H1 TCGA-EK-A2R8 
        4.47         8.28        14.50         1.81        26.27         1.45 
TCGA-EK-A2RJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A8YF TCGA-GH-A9DA TCGA-IR-A3LH 
        1.18         0.03         6.94         4.73         9.01        78.71 
TCGA-JW-A5VG TCGA-JX-A3PZ TCGA-LP-A4AX TCGA-MY-A913 TCGA-UC-A7PD TCGA-VS-A8EB 
       27.42        21.11         0.07         5.49        11.67        10.03 
TCGA-VS-A8Q9 TCGA-VS-A94X TCGA-VS-A94Y 
       46.03        16.64         4.73 

subtype1 subtype2 subtype3 
    0.10     0.03     0.03 
subtype1 subtype2 subtype3 
  137.16   195.85    99.91 
subtype1 subtype2 subtype3 
  14.925   17.850   11.440 
[1] "0.1 - 137.2 (14.9)" "0.0 - 195.8 (17.9)" "0.0 - 99.9 (11.4)" 
D4V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 32 13  1  1
  subtype2 77 27  6  2
  subtype3 14  7  1  0
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       32       77       14
  T2       13       27        7
  T3        1        6        1
  T4        1        2        0
[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"
D4V4, binary
          cls
clus        0  1
  subtype1 31 11
  subtype2 65 34
  subtype3 16  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   11
  subtype2   65   34
  subtype3   16    4
   clus
vv  subtype1 subtype2 subtype3
  0       31       65       16
  1       11       34        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 23  5 21
  subtype2 61  1 56
  subtype3 12  2 11
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       23       61       12
  M1        5        1        2
  MX       21       56       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"
          vv
clus       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             3                               19
  subtype2             1                              147
  subtype3             0                               34
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  22
  subtype2                                   0
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         2
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            5
  subtype2                                            1
  subtype3                                            0
D4V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    19      147       34
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 22        0        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            2        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         5        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"
D4V7, binary
          cls
clus         0   1
  subtype1   4  51
  subtype2  24 126
  subtype3   5  29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   51
  subtype2   24  126
  subtype3    5   29
     clus
vv    subtype1 subtype2 subtype3
  NO         4       24        5
  YES       51      126       29
[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"
D4V8, continuous
D4V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                4    12                        16
  subtype3                                2     1                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    41
  subtype2                                         1   105
  subtype3                                         0    24
D4V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        4        2
  ASIAN                                            5       12        1
  BLACK OR AFRICAN AMERICAN                        3       16        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           41      105       24
[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"
D4V11, binary
          cls
clus        0  1
  subtype1  6 34
  subtype2  9 97
  subtype3  2 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   34
  subtype2    9   97
  subtype3    2   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        9        2
  NOT HISPANIC OR LATINO       34       97       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"
D4V12, continuous
D4V13, binary
          cls
clus        0  1
  subtype1 19  6
  subtype2 49 16
  subtype3  6  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    6
  subtype2   49   16
  subtype3    6    4
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       19       49        6
  WITH TUMOR        6       16        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      4      3       1      2       2            40       3
  subtype2     12      2       0      9       3           114      10
  subtype3      4      0       0      0       2            27       1
D4V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL               4       12        4
  CANADA               3        2        0
  NIGERIA              1        0        0
  RUSSIA               2        9        0
  UKRAINE              2        3        2
  UNITED STATES       40      114       27
  VIETNAM              3       10        1
[1] 7 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 21  0  4
  subtype2  8 77 54  0  8
  subtype3  1  9 21  1  2
D4V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        8        1
  G2       24       77        9
  G3       21       54       21
  G4        0        0        1
  GX        4        8        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"
D4V16, continuous
D4V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           6
  subtype2                                          24
  subtype3                                           3
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      7
  subtype3                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              9
  subtype2                                               2             34
  subtype3                                               1              9
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  32
  subtype2                  60
  subtype3                  14
D4V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            6       24        3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        7        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                         9       34        9
  LIFELONG NON-SMOKER                                   32       60       14
[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"
D4V19, continuous
D4V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  subtype1           3       17             1        1
  subtype2          13       41            12        7
  subtype3           3       14             2        3
D4V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          3       13        3
  EXTERNAL            17       41       14
  EXTERNAL BEAM        1       12        2
  INTERNAL             1        7        3
[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"
D4V22, binary
          cls
clus        0  1
  subtype1  4  0
  subtype2 20  2
  subtype3  4  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    0
  subtype2   20    2
  subtype3    4    1
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           4       20        4
  TREATMENT NOT COMPLETED        0        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   3
  subtype2                  0                1                  16
  subtype3                  1                1                   9
          vv
clus       REGIONAL SITE
  subtype1             1
  subtype2            11
  subtype3             1
D4V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        3       16        9
  REGIONAL SITE              1       11        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"
D4V24, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 18  2
  subtype3  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   18    2
  subtype3    8    1
     clus
vv    subtype1 subtype2 subtype3
  CGY        5       18        8
  GY         0        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       7
  subtype2                                   4                      20
  subtype3                                   1                       5
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       5
  subtype3                       0                       1
D4V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        4        1
  OTHER LOCATION, SPECIFY                    7       20        5
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        5        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                                             0
  subtype2                                             2
  subtype3                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              4
  subtype2                                             10
  subtype3                                              1
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                16
  subtype2                                                                                48
  subtype3                                                                                 1
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           27
  subtype2                                                                                           60
  subtype3                                                                                           18
D4V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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)                  16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                     10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       60
                                                                                              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)                   1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       18
[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"
D4V33, binary
          cls
clus        0  1
  subtype1 21 19
  subtype2 37 45
  subtype3  9  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   19
  subtype2   37   45
  subtype3    9    7
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        21       37        9
  PRESENT       19       45        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"
D4V34, continuous
D4V35, continuous
D4V36, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2 40 67
  subtype3  7 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2   40   67
  subtype3    7   14
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            1       40        7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       13       67       14
[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"
D4V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          15         12
  subtype2            2          29         36
  subtype3            3           3          8
D4V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        5        2        3
  FORMER USER        15       29        3
  NEVER USED         12       36        8
[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"
D4V39, continuous
D4V40, binary
          cls
clus        0  1
  subtype1 31  4
  subtype2 52 12
  subtype3 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    4
  subtype2   52   12
  subtype3   10    0
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        31       52       10
  PRESENT        4       12        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         2     0
  subtype2           2        12     0
  subtype3           0         3     1
D4V41, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       14        4 
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
             clus
vv            subtype2 subtype3
  CARBOPLATIN        2        0
  CISPLATIN         12        3
  OTHER              0        1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        9        3 
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    0   3   23    6  1   2    2    3   5  0   1  1   0  2
  subtype2   1    1  20   39   16  3   5    2    6  11  1   5  2   0 10
  subtype3   0    0   9    2    3  0   1    3    1   2  0   1  0   1  3
D4V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        1        0
  T1A1        0        1        0
  T1B         3       20        9
  T1B1       23       39        2
  T1B2        6       16        3
  T2          1        3        0
  T2A         2        5        1
  T2A1        2        2        3
  T2A2        3        6        1
  T2B         5       11        2
  T3          0        1        0
  T3B         1        5        1
  T4          1        2        0
  TIS         0        0        1
  TX          2       10        3
[1] 15  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        3        24         8
  subtype2       3        2         1         1       23        37        18
  subtype3       0        0         0         0        8         6         8
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         1          1          2         5         0
  subtype2        3         3          2          4        15         1
  subtype3        0         2          2          1         3         0
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1          5         0         4
  subtype2         25         4         3
  subtype3          3         0         0
D4V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        3        0
  STAGE IA          0        2        0
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          3       23        8
  STAGE IB1        24       37        6
  STAGE IB2         8       18        8
  STAGE II          1        3        0
  STAGE IIA         1        3        2
  STAGE IIA1        1        2        2
  STAGE IIA2        2        4        1
  STAGE IIB         5       15        3
  STAGE III         0        1        0
  STAGE IIIB        5       25        3
  STAGE IVA         0        4        0
  STAGE IVB         4        3        0
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 63 16
  subtype2 54 11
  subtype3 74 27
subtype1 subtype2 subtype3 
      79       65      101 
subtype1 subtype2 subtype3 
      16       11       27 
$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-A1ML TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2M1 TCGA-C5-A2M2 
       35.61        20.91        33.90        44.22        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-C5-A902 TCGA-C5-A905 
       18.02        20.35         2.73        27.52         4.90       160.41 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3QD 
        1.12        58.88        50.76        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-A2RA TCGA-EK-A2RL 
       14.96        13.58       113.16         0.59        16.08        23.70 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        2.24         0.10        14.70        19.79         4.73         1.22 
TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA 
        1.02         1.35         1.32         1.12         9.44       137.16 
TCGA-IR-A3LB TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q8 
       66.81        81.96         3.29        10.06         6.71        30.31 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        7.99         0.30         0.20        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        2.96        15.58        16.14        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ 
       10.39        61.28        10.03        34.52        29.03        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       32.15        23.28        11.51        44.88        42.58        42.08 
TCGA-VS-A959 
       39.35 

$subtype2
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1M5 TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A3HF 
       49.48        23.67        67.46         0.46         3.58        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE 
       20.42       182.93       101.82       134.33       147.35        85.55 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 
       50.99         8.35        75.78         6.12        20.91        17.03 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1OA TCGA-DS-A1OD 
       44.94        40.04        58.88        36.76        28.90       127.36 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       16.83        17.52         0.76         1.32         0.82         0.62 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R 
        1.35        12.66         0.26        15.02        14.99        13.48 
TCGA-EA-A97N TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RO TCGA-EX-A1H5 
        0.36         1.45         0.13         4.04         0.07        20.35 
TCGA-EX-A1H6 TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        7.92         2.17         1.45         1.48         0.82         3.52 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
       25.41         7.13        21.67        20.78        14.93       147.39 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y 
      117.40        96.95        78.71        11.28         0.89        13.87 
TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8QM 
        0.03        13.35        93.99        12.16        31.27 

$subtype3
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1MH 
      177.04       173.29         5.46        19.86        46.32        38.99 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        2.43        40.93        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH 
      100.14        52.01       154.32        15.48        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ 
       94.95         9.34        13.61        45.83        99.91        23.51 
TCGA-C5-A907 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
        4.47        87.75         2.66       117.99       118.65         8.75 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HU 
       28.31        12.36        22.98        12.36         1.74         2.66 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
        1.18        14.50         1.81        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RB TCGA-EK-A2RD 
        6.64         1.51         0.43         0.59         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 
        0.36         1.18         0.10         0.10         0.03         6.94 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A5XV 
        6.12        23.84         0.92         0.66         1.58         1.97 
TCGA-GH-A9DA TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
        9.01        26.56        36.36        27.42        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AX 
       20.48        15.58         5.13        21.11       195.85         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        15.95         3.39        17.56 
TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EH TCGA-VS-A8EI 
       14.07        19.59         3.88        11.67        20.22        14.07 
TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94X 
       27.25        53.52        46.03        49.55        39.78        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        23.24        43.82        38.96        18.05 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  160.41   182.93   195.85 
subtype1 subtype2 subtype3 
   15.58    15.02    17.56 
[1] "0.1 - 160.4 (15.6)" "0.0 - 182.9 (15.0)" "0.0 - 195.8 (17.6)"
D5V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 45 20  4  1
  subtype2 38 14  1  1
  subtype3 44 18  4  2
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       45       38       44
  T2       20       14       18
  T3        4        1        4
  T4        1        1        2
[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"
D5V4, binary
          cls
clus        0  1
  subtype1 42 17
  subtype2 35 18
  subtype3 40 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   17
  subtype2   35   18
  subtype3   40   16
   clus
vv  subtype1 subtype2 subtype3
  0       42       35       40
  1       17       18       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"
          vv
clus       M0 M1 MX
  subtype1 34  6 33
  subtype2 30  1 25
  subtype3 35  1 38
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       34       30       35
  M1        6        1        1
  MX       33       25       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             4                               47
  subtype2             1                               60
  subtype3             0                              102
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             1
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  17
  subtype2                                   5
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            4
  subtype2                                            1
  subtype3                                            1
D5V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    47       60      102
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 17        5        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         4        1        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  8 71
  subtype2  8 60
  subtype3 19 84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   71
  subtype2    8   60
  subtype3   19   84
     clus
vv    subtype1 subtype2 subtype3
  NO         8        8       19
  YES       71       60       84
[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                                1     8                         7
  subtype2                                1     7                         6
  subtype3                                6     4                        13
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    54
  subtype2                                         0    48
  subtype3                                         1    76
D5V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        6
  ASIAN                                            8        7        4
  BLACK OR AFRICAN AMERICAN                        7        6       13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           54       48       76
[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  7 49
  subtype2  2 47
  subtype3  8 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   49
  subtype2    2   47
  subtype3    8   61
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        2        8
  NOT HISPANIC OR LATINO       49       47       61
[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 26  9
  subtype2 22  5
  subtype3 27 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    9
  subtype2   22    5
  subtype3   27   14
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       26       22       27
  WITH TUMOR        9        5       14
[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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     11      3       1      2       3            54       5
  subtype2      1      2       0      5       2            52       6
  subtype3     12      0       0      4       2            82       3
D5V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              11        1       12
  CANADA               3        2        0
  NIGERIA              1        0        0
  RUSSIA               2        5        4
  UKRAINE              3        2        2
  UNITED STATES       54       52       82
  VIETNAM              5        6        3
[1] 7 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  7 30 35  0  7
  subtype2  8 34 23  1  1
  subtype3  2 49 44  0  6
D5V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        7        8        2
  G2       30       34       49
  G3       35       23       44
  G4        0        1        0
  GX        7        1        6
[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                                           9
  subtype2                                           8
  subtype3                                          16
          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             13
  subtype2                                               2             18
  subtype3                                               1             23
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  46
  subtype2                  29
  subtype3                  39
D5V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            9        8       16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        3        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        2        1
  CURRENT SMOKER                                        13       18       23
  LIFELONG NON-SMOKER                                   46       29       39
[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
D5V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           6       30             2        0        2
  subtype2           2       18             6        1        3
  subtype3          12       29             7        0        7
D5V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          6        2       12
  EXTERNAL            30       18       29
  EXTERNAL BEAM        2        6        7
  IMPLANTS             0        1        0
  INTERNAL             2        3        7
[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"
D5V22, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2  6  0
  subtype3 15  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2    6    0
  subtype3   15    3
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           8        6       15
  TREATMENT NOT COMPLETED        0        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   3
  subtype2                  0                1                   8
  subtype3                  1                1                  19
          vv
clus       REGIONAL SITE
  subtype1             7
  subtype2             3
  subtype3             6
D5V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        3        8       19
  REGIONAL SITE              7        3        6
[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"
D5V24, binary
          cls
clus        0  1
  subtype1 11  0
  subtype2  8  0
  subtype3 17  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    0
  subtype2    8    0
  subtype3   17    3
     clus
vv    subtype1 subtype2 subtype3
  CGY       11        8       17
  GY         0        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V25, continuous
D5V26, continuous
D5V27, continuous
D5V28, continuous
D5V29, continuous
D5V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   2                       8
  subtype2                                   2                      11
  subtype3                                   3                      14
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       5
  subtype3                       0                       2
D5V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        2        2        3
  OTHER LOCATION, SPECIFY                    8       11       14
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    2        5        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                                              8
  subtype2                                              3
  subtype3                                              5
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                19
  subtype2                                                                                23
  subtype3                                                                                28
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           37
  subtype2                                                                                           26
  subtype3                                                                                           46
D5V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       37
                                                                                              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)       26
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       46
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V33, binary
          cls
clus        0  1
  subtype1 24 29
  subtype2 21 26
  subtype3 24 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   29
  subtype2   21   26
  subtype3   24   21
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        24       21       24
  PRESENT       29       26       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"
D5V34, continuous
D5V35, continuous
D5V36, binary
          cls
clus        0  1
  subtype1  4 25
  subtype2 18 25
  subtype3 27 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   25
  subtype2   18   25
  subtype3   27   47
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            4       18       27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       25       25       47
[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"
D5V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          18         20
  subtype2            2          15         15
  subtype3            3          16         27
D5V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        5        2        3
  FORMER USER        18       15       16
  NEVER USED         20       15       27
[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"
D5V39, continuous
D5V40, binary
          cls
clus        0  1
  subtype1 34  7
  subtype2 31  6
  subtype3 31  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    7
  subtype2   31    6
  subtype3   31    4
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        34       31       31
  PRESENT        7        6        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         3     0
  subtype2           1         3     0
  subtype3           2        12     1
D5V41, multiclass
             clus
vv            subtype1 subtype2 subtype3
  CARBOPLATIN        0        1        2
  CISPLATIN          3        3       12
  OTHER              0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        4        7 
 [1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    0   8   29    8  2   3    3    6   6  0   4  1   0  3
  subtype2   0    1   6   23    8  1   3    2    2   6  0   1  1   0  3
  subtype3   1    0  18   16    9  1   2    2    2  11  1   3  2   1  9
D5V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         0        0        1
  T1A1        0        1        0
  T1B         8        6       18
  T1B1       29       23       16
  T1B2        8        8        9
  T2          2        1        1
  T2A         3        3        2
  T2A1        3        2        2
  T2A2        6        2        2
  T2B         6        6       11
  T3          0        0        1
  T3B         4        1        3
  T4          1        1        2
  TIS         0        0        1
  TX          3        3        9
[1] 15  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       2        0         0         0        7        28        13
  subtype2       0        1         1         1        7        24         9
  subtype3       2        1         0         0       21        18        12
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         1          1          5         5         0
  subtype2        1         3          2          2         5         0
  subtype3        2         3          2          0        17         1
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1         11         1         4
  subtype2          7         2         1
  subtype3         16         2         2
D5V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        2
  STAGE IA          0        1        1
  STAGE IA1         0        1        0
  STAGE IA2         0        1        0
  STAGE IB          7        7       21
  STAGE IB1        28       24       18
  STAGE IB2        13        9       12
  STAGE II          1        1        2
  STAGE IIA         1        3        3
  STAGE IIA1        1        2        2
  STAGE IIA2        5        2        0
  STAGE IIB         5        5       17
  STAGE III         0        0        1
  STAGE IIIB       11        7       16
  STAGE IVA         1        2        2
  STAGE IVB         4        1        2
[1] 16  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 38  9
  subtype2 63 16
  subtype3 50 13
  subtype4 13  5
  subtype5 27 11
subtype1 subtype2 subtype3 subtype4 subtype5 
      47       79       63       18       38 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       16       13        5       11 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LS TCGA-C5-A2M1 
       31.40        57.73        35.61         0.46        44.22        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A7CM TCGA-C5-A7X8 TCGA-C5-A8YT TCGA-DG-A2KH 
        0.82        17.85        20.35         2.73         6.12         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A4BA 
       58.88        50.76        16.18        17.52        14.50        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H6 
       14.89         1.48        23.70         2.24         0.10         7.92 
TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A40J TCGA-FU-A57G 
       14.70         4.73         1.22         2.17         1.35         1.32 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JW-A69B 
        1.12         9.44       137.16        66.81        96.95        10.06 
TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
       30.31         0.20        15.58        16.14        15.88         6.25 
TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A952 
       10.39        61.28        23.28        39.78        44.88 

$subtype2
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML TCGA-C5-A2LX 
       82.85        19.86        30.21        53.16        20.91        83.05 
TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
      100.14       154.32        15.48        60.69        94.95        13.61 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8ZZ 
       45.83         8.35        75.78        99.91        23.51        20.91 
TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-EA-A3HR 
       17.03         4.90       160.41        28.31        22.98         1.32 
TCGA-EA-A3HU TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5O9 
        2.66         1.18         1.35        12.66         0.26        13.91 
TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 
       13.58        12.59       113.16         1.51         0.59         0.59 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RN TCGA-EK-A3GN TCGA-EX-A69L 
       16.08         0.03         0.36         0.10         0.03        19.79 
TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A5XV 
        6.12         0.92         0.66         1.58         0.82         1.97 
TCGA-HG-A9SC TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 
        7.13        81.96        24.56        21.44        20.48         5.13 
TCGA-JW-AAVH TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A8JM TCGA-MY-A5BD 
        6.71         7.99         0.30         0.82         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-UC-A7PG 
        4.34        15.95        17.56        14.07         5.88        12.16 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EK TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC 
       29.03        20.22        27.25        53.52        32.15        11.51 
TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       23.24        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

$subtype3
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 
       49.48        23.67        68.84        36.56       177.04        67.46 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LY 
       46.32        38.99         2.43        40.93         3.58        78.35 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE 
       20.42       182.93       101.82       134.33       147.35        85.55 
TCGA-C5-A7XC TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.99        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A5RQ TCGA-EA-A1QS 
        2.66       117.99         8.75        28.90        16.83         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5ZD 
       12.36         1.74         0.82         0.62        13.05        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       14.99        13.48         0.36         1.45         0.13         4.04 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.07        20.35         1.45         3.52        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LK TCGA-IR-A3LL 
       20.78        14.93       147.39       117.40        26.56        36.36 
TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-R2-A69V 
        0.89        13.87         0.03         0.07        13.35        19.59 
TCGA-UC-A7PF TCGA-VS-A8Q9 TCGA-VS-A8QM 
       93.99        46.03        31.27 

$subtype4
TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A7X3 TCGA-C5-A8YR TCGA-DS-A0VN TCGA-DS-A1OC 
       57.04       173.29         9.34        27.52       118.65        12.36 
TCGA-EA-A410 TCGA-EA-A5ZF TCGA-EK-A2RB TCGA-EK-A2RJ TCGA-FU-A23L TCGA-FU-A3HZ 
        1.35        14.96         0.07         1.18        23.84         1.02 
TCGA-JW-A5VH TCGA-JX-A3Q0 TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-VS-A8EC TCGA-VS-A94X 
        3.29       195.85         2.96         3.39        34.52        16.64 

$subtype5
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MQ 
       11.44        18.74       144.16         5.46        35.01        33.90 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7UC TCGA-C5-A907 
       73.18        73.45        52.01        18.02        17.19         4.47 
TCGA-DS-A1OD TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EK-A2H0 TCGA-EK-A2H1 
      127.36         8.28        14.50         1.81        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-FU-A3TX TCGA-GH-A9DA 
        6.64         0.43         0.10         6.94         1.48         9.01 
TCGA-IR-A3LH TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AX 
       78.71        27.42        15.58        21.11        11.28         0.07 
TCGA-MY-A913 TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ 
        5.49         3.88        11.67        10.03        14.07        19.96 
TCGA-VS-A8QF TCGA-VS-A94Y 
       49.55         4.73 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.03     0.03     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  137.16   160.41   182.93   195.85   144.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.890   16.080   21.670   13.660   14.285 
[1] "0.1 - 137.2 (14.9)" "0.0 - 160.4 (16.1)" "0.0 - 182.9 (21.7)"
[4] "0.1 - 195.8 (13.7)" "0.1 - 144.2 (14.3)"
D6V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 31  8  0  0
  subtype2 28 23  4  2
  subtype3 44  8  0  1
  subtype4  8  5  2  1
  subtype5 16  8  3  0
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       31       28       44        8       16
  T2        8       23        8        5        8
  T3        0        4        0        2        3
  T4        0        2        1        1        0
[1] 4 5
[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 28  9
  subtype2 27 18
  subtype3 34 17
  subtype4 10  2
  subtype5 18  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    9
  subtype2   27   18
  subtype3   34   17
  subtype4   10    2
  subtype5   18    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       28       27       34       10       18
  1        9       18       17        2        5
[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"
          vv
clus       M0 M1 MX
  subtype1 17  2 22
  subtype2 21  1 39
  subtype3 33  1 21
  subtype4 12  1  4
  subtype5 16  3 10
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       17       21       33       12       16
  M1        2        1        1        1        3
  MX       22       39       21        4       10
[1] 3 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       ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  subtype1             4                               11
  subtype2             1                               76
  subtype3             0                               64
  subtype4             0                               20
  subtype5             0                               38
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  20
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   1
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            6
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
  subtype5                                            0
D6V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    11       76       64
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        1        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20        1        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         6        0        0
                                               clus
vv                                              subtype4 subtype5
  ADENOSQUAMOUS                                        0        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    20       38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0        0
[1] 6 5
[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  3 45
  subtype2  7 72
  subtype3 12 52
  subtype4  3 17
  subtype5 10 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   45
  subtype2    7   72
  subtype3   12   52
  subtype4    3   17
  subtype5   10   29
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         3        7       12        3       10
  YES       45       72       52       17       29
[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"
D6V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       29       19        2       11 
 [1] "subtype3" "subtype5" "subtype3" "subtype5" "subtype5" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype5" "subtype5" "subtype2" "subtype2"
[19] "subtype1" "subtype5" "subtype1" "subtype3" "subtype3" "subtype2"
[25] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[43] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype1" "subtype5" "subtype3"
[55] "subtype1" "subtype3" "subtype1" "subtype5" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype5" "subtype5" "subtype2" "subtype2" "subtype3" "subtype5"
[73] "subtype2" "subtype2"
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         2
  subtype2                                3     5                        11
  subtype3                                1     6                         6
  subtype4                                1     2                         3
  subtype5                                3     2                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    37
  subtype2                                         0    53
  subtype3                                         0    46
  subtype4                                         0    14
  subtype5                                         1    28
D6V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        3        1        1
  ASIAN                                            4        5        6        2
  BLACK OR AFRICAN AMERICAN                        2       11        6        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        0
  WHITE                                           37       53       46       14
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 3
  ASIAN                                            2
  BLACK OR AFRICAN AMERICAN                        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           28
[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"
D6V11, binary
          cls
clus        0  1
  subtype1  4 30
  subtype2  7 46
  subtype3  1 48
  subtype4  2 14
  subtype5  3 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   30
  subtype2    7   46
  subtype3    1   48
  subtype4    2   14
  subtype5    3   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        7        1        2        3
  NOT HISPANIC OR LATINO       30       46       48       14       19
[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"
D6V12, continuous
D6V13, binary
          cls
clus        0  1
  subtype1 17  5
  subtype2 15  8
  subtype3 26  8
  subtype4  5  2
  subtype5 12  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    5
  subtype2   15    8
  subtype3   26    8
  subtype4    5    2
  subtype5   12    5
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  TUMOR FREE       17       15       26        5       12
  WITH TUMOR        5        8        8        2        5
[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"
          vv
clus       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      3      3       0      1       2            37       2
  subtype2     12      0       0      4       2            57       4
  subtype3      2      2       0      5       1            50       4
  subtype4      2      0       1      1       0            14       2
  subtype5      5      0       0      0       2            30       2
D6V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  BRAZIL               3       12        2        2        5
  CANADA               3        0        2        0        0
  NIGERIA              0        0        0        1        0
  RUSSIA               1        4        5        1        0
  UKRAINE              2        2        1        0        2
  UNITED STATES       37       57       50       14       30
  VIETNAM              2        4        4        2        2
[1] 7 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       G1 G2 G3 G4 GX
  subtype1  6 21 17  0  4
  subtype2  3 40 30  0  4
  subtype3  6 31 26  0  1
  subtype4  0 12  7  0  1
  subtype5  2  9 22  1  4
D6V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  G1        6        3        6        0        2
  G2       21       40       31       12        9
  G3       17       30       26        7       22
  G4        0        0        0        0        1
  GX        4        4        1        1        4
[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"
D6V16, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       12        7        2        7 
 [1] "subtype3" "subtype5" "subtype2" "subtype1" "subtype2" "subtype3"
 [7] "subtype1" "subtype5" "subtype1" "subtype3" "subtype2" "subtype5"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype5"
[19] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype5"
[25] "subtype3" "subtype2" "subtype2" "subtype1" "subtype5" "subtype5"
[31] "subtype2" "subtype2"
D6V17, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       29       19        2       11 
 [1] "subtype3" "subtype5" "subtype3" "subtype5" "subtype5" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype5" "subtype5" "subtype2" "subtype2"
[19] "subtype1" "subtype5" "subtype1" "subtype3" "subtype3" "subtype2"
[25] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[43] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype1" "subtype5" "subtype3"
[55] "subtype1" "subtype3" "subtype1" "subtype5" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype5" "subtype5" "subtype2" "subtype2" "subtype3" "subtype5"
[73] "subtype2" "subtype2"
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           6
  subtype2                                          12
  subtype3                                           4
  subtype4                                           3
  subtype5                                           8
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      2
  subtype3                                      5
  subtype4                                      0
  subtype5                                      0
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0             10
  subtype2                                               1             18
  subtype3                                               1             16
  subtype4                                               0              2
  subtype5                                               1              8
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  26
  subtype2                  31
  subtype3                  31
  subtype4                  11
  subtype5                  15
D6V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            6       12        4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        1
  CURRENT SMOKER                                        10       18       16
  LIFELONG NON-SMOKER                                   26       31       31
                                                 clus
vv                                                subtype4 subtype5
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            3        8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 0        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1
  CURRENT SMOKER                                         2        8
  LIFELONG NON-SMOKER                                   11       15
[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"
D6V19, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       25       14        2       13 
 [1] "subtype3" "subtype3" "subtype5" "subtype5" "subtype2" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype5" "subtype5"
[13] "subtype2" "subtype2" "subtype1" "subtype5" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype5" "subtype2" "subtype3" "subtype2"
[43] "subtype1" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
[49] "subtype5" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype1" "subtype5" "subtype5" "subtype2"
[61] "subtype2" "subtype5" "subtype3" "subtype5" "subtype2" "subtype2"
D6V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           3       16             0        0        1
  subtype2           4       27             3        0        7
  subtype3           7       15             5        1        1
  subtype4           1        5             2        0        1
  subtype5           5       14             5        0        2
D6V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4 subtype5
  COMBINATION          3        4        7        1        5
  EXTERNAL            16       27       15        5       14
  EXTERNAL BEAM        0        3        5        2        5
  IMPLANTS             0        0        1        0        0
  INTERNAL             1        7        1        1        2
[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"
D6V22, binary
          cls
clus       0 1
  subtype1 3 0
  subtype2 7 0
  subtype3 9 1
  subtype4 2 0
  subtype5 8 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    7    0
  subtype3    9    1
  subtype4    2    0
  subtype5    8    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  COMPLETED AS PLANNED           3        7        9        2        8
  TREATMENT NOT COMPLETED        0        0        1        0        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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   3
  subtype2                  0                0                  13
  subtype3                  0                1                   6
  subtype4                  0                0                   2
  subtype5                  1                1                   6
          vv
clus       REGIONAL SITE
  subtype1             1
  subtype2            11
  subtype3             1
  subtype4             2
  subtype5             1
D6V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3 subtype4 subtype5
  DISTANT RECURRENCE         1        0        0        0        1
  LOCAL RECURRENCE           0        0        1        0        1
  PRIMARY TUMOR FIELD        3       13        6        2        6
  REGIONAL SITE              1       11        1        2        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V24, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 16  1
  subtype3  5  1
  subtype4  3  0
  subtype5  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   16    1
  subtype3    5    1
  subtype4    3    0
  subtype5    7    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  CGY        5       16        5        3        7
  GY         0        1        1        0        1
[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"
D6V25, continuous
D6V26, continuous
D6V27, continuous
D6V28, continuous
D6V29, continuous
D6V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   1
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
  subtype5                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   0                       5
  subtype2                                   2                       7
  subtype3                                   3                      12
  subtype4                                   0                       2
  subtype5                                   2                       7
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       3
  subtype3                       0                       3
  subtype4                       0                       0
  subtype5                       0                       1
D6V31, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       13       19        2       10 
 [1] "subtype3" "subtype5" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype2" "subtype5" "subtype1" "subtype2" "subtype1" "subtype3"
[13] "subtype5" "subtype1" "subtype5" "subtype5" "subtype2" "subtype1"
[19] "subtype5" "subtype3" "subtype3" "subtype5" "subtype1" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype5"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[43] "subtype1" "subtype3" "subtype5" "subtype2" "subtype3" "subtype2"
[49] "subtype5" "subtype1"
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype5
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        1        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        0        2        3        2
  OTHER LOCATION, SPECIFY                    5        7       12        7
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        3        3        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                                             0
  subtype2                                             1
  subtype3                                             1
  subtype4                                             0
  subtype5                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              2
  subtype2                                              7
  subtype3                                              4
  subtype4                                              2
  subtype5                                              1
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                13
  subtype2                                                                                23
  subtype3                                                                                28
  subtype4                                                                                 4
  subtype5                                                                                 2
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           25
  subtype2                                                                                           31
  subtype3                                                                                           21
  subtype4                                                                                            7
  subtype5                                                                                           25
D6V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  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)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       25
                                                                                              clus
vv                                                                                             subtype2
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      7
  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)       31
                                                                                              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)                  28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       21
                                                                                              clus
vv                                                                                             subtype4
  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)        7
                                                                                              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)                   2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       25
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V33, binary
          cls
clus        0  1
  subtype1 20 15
  subtype2 17 22
  subtype3 18 28
  subtype4  5  3
  subtype5  9  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   15
  subtype2   17   22
  subtype3   18   28
  subtype4    5    3
  subtype5    9    8
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        20       17       18        5        9
  PRESENT       15       22       28        3        8
[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"
D6V34, continuous
D6V35, continuous
D6V36, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2 18 34
  subtype3 19 27
  subtype4  3 11
  subtype5  9 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2   18   34
  subtype3   19   27
  subtype4    3   11
  subtype5    9   15
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       18       19        3
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       10       34       27       11
                                          clus
vv                                         subtype5
  KERATINIZING SQUAMOUS CELL CARCINOMA            9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       15
[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"
D6V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            4          13         10
  subtype2            2          15         22
  subtype3            1          13         17
  subtype4            0           4          4
  subtype5            3           4          9
D6V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4 subtype5
  CURRENT USER        4        2        1        0        3
  FORMER USER        13       15       13        4        4
  NEVER USED         10       22       17        4        9
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V39, continuous
D6V40, binary
          cls
clus        0  1
  subtype1 27  3
  subtype2 21  5
  subtype3 31  7
  subtype4  5  2
  subtype5 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    3
  subtype2   21    5
  subtype3   31    7
  subtype4    5    2
  subtype5   12    0
         clus
vv        subtype1 subtype2 subtype3 subtype4 subtype5
  ABSENT        27       21       31        5       12
  PRESENT        3        5        7        2        0
[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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         1     0
  subtype2           1         2     0
  subtype3           2         7     0
  subtype4           0         1     0
  subtype5           0         7     1
D6V41, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        3        9        1        8 
 [1] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype3"
 [7] "subtype3" "subtype5" "subtype5" "subtype2" "subtype3" "subtype5"
[13] "subtype3" "subtype3" "subtype2" "subtype5" "subtype2" "subtype5"
[19] "subtype5" "subtype3"
             clus
vv            subtype2 subtype3 subtype5
  CARBOPLATIN        1        2        0
  CISPLATIN          2        7        7
  OTHER              0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype5 
       1        3        6        3 
 [1] "subtype5" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [7] "subtype5" "subtype3" "subtype2" "subtype3" "subtype2" "subtype5"
          vv
clus       T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS TX
  subtype1   0    0   3   23    5  1   2    3    1   1  0   0  0   0  2
  subtype2   1    0   6   13    8  2   2    0    6  13  0   4  2   0  7
  subtype3   0    1  12   24    7  0   3    1    0   4  0   0  1   0  3
  subtype4   0    0   3    3    2  0   0    1    2   2  1   1  1   0  1
  subtype5   0    0   8    5    3  1   1    2    1   3  0   3  0   1  2
D6V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4 subtype5
  T1A         0        1        0        0        0
  T1A1        0        0        1        0        0
  T1B         3        6       12        3        8
  T1B1       23       13       24        3        5
  T1B2        5        8        7        2        3
  T2          1        2        0        0        1
  T2A         2        2        3        0        1
  T2A1        3        0        1        1        2
  T2A2        1        6        0        2        1
  T2B         1       13        4        2        3
  T3          0        0        0        1        0
  T3B         0        4        0        1        3
  T4          0        2        1        1        0
  TIS         0        0        0        0        1
  TX          2        7        3        1        2
[1] 15  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1 STAGE IB2
  subtype1       1        0         0         0        2        25         8
  subtype2       2        1         0         0        7        15        10
  subtype3       0        1         1         1       13        21         8
  subtype4       1        0         0         0        6         1         1
  subtype5       0        0         0         0        7         8         7
          vv
clus       STAGE II STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE III
  subtype1        1         1          1          0         2         0
  subtype2        2         1          0          3        13         0
  subtype3        1         2          1          1         2         0
  subtype4        0         0          1          2         2         1
  subtype5        0         3          2          1         8         0
          vv
clus       STAGE IIIB STAGE IVA STAGE IVB
  subtype1          5         0         2
  subtype2         15         3         2
  subtype3          8         2         1
  subtype4          3         0         2
  subtype5          3         0         0
D6V45, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        2        0        1        0
  STAGE IA          0        1        1        0        0
  STAGE IA1         0        0        1        0        0
  STAGE IA2         0        0        1        0        0
  STAGE IB          2        7       13        6        7
  STAGE IB1        25       15       21        1        8
  STAGE IB2         8       10        8        1        7
  STAGE II          1        2        1        0        0
  STAGE IIA         1        1        2        0        3
  STAGE IIA1        1        0        1        1        2
  STAGE IIA2        0        3        1        2        1
  STAGE IIB         2       13        2        2        8
  STAGE III         0        0        0        1        0
  STAGE IIIB        5       15        8        3        3
  STAGE IVA         0        3        2        0        0
  STAGE IVB         2        2        1        2        0
[1] 16  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 82 16
  subtype2 52 13
  subtype3 49 23
subtype1 subtype2 subtype3 
      98       65       72 
subtype1 subtype2 subtype3 
      16       13       23 
$subtype1
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       31.40        35.01        57.73        38.43         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
       18.02       182.93       154.32        20.35        17.19        60.69 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       13.61         2.73         8.35        99.91        23.51        27.52 
TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        4.90       160.41         4.47         1.12        58.88        50.76 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA 
       16.18         8.28        14.50         1.35         1.81        12.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IR TCGA-EK-A2PG 
       14.89         1.48        14.96        12.59       113.16         1.51 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN 
        0.59         1.18        23.70         2.24         0.10         0.03 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A40J 
       19.79         6.12         4.73         0.92         1.02         1.35 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LI TCGA-JW-A5VG 
        1.97         1.12         9.44       137.16        81.96        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
        5.13         6.71        30.31         7.99        11.28         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.30         0.82         0.20        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.49         2.96        15.58        15.95        16.14        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-UC-A7PI TCGA-VS-A8EB 
       15.88         5.88         6.25        10.39        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EK TCGA-VS-A8Q9 
       34.52        29.03        20.22        19.96        27.25        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
       23.28        49.55        39.78        44.88        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

$subtype2
TCGA-C5-A1BF TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A3HF TCGA-C5-A3HL 
       18.74         0.46         3.58        44.22        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A7XC 
      101.82       134.33        15.48       147.35         9.34        50.99 
TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A901 TCGA-DG-A2KL TCGA-DR-A0ZM 
       75.78         6.12        20.91        17.03        44.94        58.88 
TCGA-DS-A0VK TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       36.76        16.83        17.52         0.76         1.74         1.32 
TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD 
        0.62         1.35        14.50        12.66         0.26        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2PM TCGA-EK-A2R8 
       14.99        13.48         0.36        26.27         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RO TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A3EO 
        0.13         4.04         0.07         7.92         6.94         2.17 
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-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LB 
        7.13        21.67        20.78        14.93       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A8JM TCGA-Q1-A5R2 
      117.40        96.95         0.89        13.87         5.42        13.35 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QM TCGA-WL-A834 
       93.99        14.07        11.51        31.27        18.05 

$subtype3
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK 
       46.32        30.21        53.16        38.99        35.61         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MQ TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93        33.90        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XH TCGA-DG-A2KM 
       78.35       100.14        85.55        94.95        45.83        40.04 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA 
       87.75         2.66       117.99       118.65         8.75        28.90 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HS 
       28.31        12.36       127.36        22.98        12.36         0.82 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP 
        2.66        13.05         1.18        13.58        45.96         6.64 
TCGA-EK-A2PL TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A3GJ TCGA-FU-A23K TCGA-FU-A23L 
        0.43        16.08         0.07         0.10         1.22        23.84 
TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
        0.66         1.58         9.01        78.71        26.56        36.36 
TCGA-JX-A3PZ TCGA-Q1-A6DT TCGA-Q1-A73O TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       21.11         3.39        14.07        19.59         3.88        11.67 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 
       53.52        32.15        16.64         4.73        23.24        42.58 

subtype1 subtype2 subtype3 
    0.03     0.07     0.07 
subtype1 subtype2 subtype3 
  182.93   147.39   177.04 
subtype1 subtype2 subtype3 
  15.580   14.070   28.605 
[1] "0.0 - 182.9 (15.6)" "0.1 - 147.4 (14.1)" "0.1 - 177.0 (28.6)"
D7V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 46 23  4  2
  subtype2 34 13  1  1
  subtype3 42 13  2  1
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       46       34       42
  T2       23       13       13
  T3        4        1        2
  T4        2        1        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"
D7V4, binary
          cls
clus        0  1
  subtype1 43 15
  subtype2 36 13
  subtype3 33 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   15
  subtype2   36   13
  subtype3   33   20
   clus
vv  subtype1 subtype2 subtype3
  0       43       36       33
  1       15       13       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"
          vv
clus       M0 M1 MX
  subtype1 35  6 41
  subtype2 27  1 24
  subtype3 34  0 25
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       35       27       34
  M1        6        1        0
  MX       41       24       25
[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             4                               70
  subtype2             1                               57
  subtype3             0                               72
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             3
  subtype2                                             2
  subtype3                                             0
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  14
  subtype2                                   7
  subtype3                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            5
  subtype2                                            1
  subtype3                                            0
D7V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        4        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    70       57       72
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        3        2        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 14        7        0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         5        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  3 96
  subtype2  6 62
  subtype3 24 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   96
  subtype2    6   62
  subtype3   24   48
     clus
vv    subtype1 subtype2 subtype3
  NO         3        6       24
  YES       96       62       48
[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                                5     9                        13
  subtype2                                1     6                         2
  subtype3                                1     3                         8
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    64
  subtype2                                         0    54
  subtype3                                         1    54
D7V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 5        1        1
  ASIAN                                            9        6        3
  BLACK OR AFRICAN AMERICAN                       13        2        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                           64       54       54
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
          cls
clus        0  1
  subtype1 12 58
  subtype2  2 46
  subtype3  3 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   58
  subtype2    2   46
  subtype3    3   44
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12        2        3
  NOT HISPANIC OR LATINO       58       46       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, continuous
D7V13, binary
          cls
clus        0  1
  subtype1 25  9
  subtype2 17  4
  subtype3 30 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    9
  subtype2   17    4
  subtype3   30   14
            clus
vv           subtype1 subtype2 subtype3
  TUMOR FREE       25       17       30
  WITH TUMOR        9        4       14
[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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1     15      3       1      2       4            68       6
  subtype2      3      1       0      5       2            51       6
  subtype3      6      1       0      4       0            60       1
D7V14, multiclass
               clus
vv              subtype1 subtype2 subtype3
  BRAZIL              15        3        6
  CANADA               3        1        1
  NIGERIA              1        0        0
  RUSSIA               2        5        4
  UKRAINE              4        2        0
  UNITED STATES       68       51       60
  VIETNAM              6        6        1
[1] 7 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 36 49  0  8
  subtype2  8 35 22  0  2
  subtype3  1 35 29  1  4
D7V15, multiclass
    clus
vv   subtype1 subtype2 subtype3
  G1        6        8        1
  G2       36       35       35
  G3       49       22       29
  G4        0        0        1
  GX        8        2        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"
D7V16, continuous
D7V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                          12
  subtype2                                           7
  subtype3                                          13
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      3
  subtype3                                      3
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               1             14
  subtype2                                               2             18
  subtype3                                               0             19
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  53
  subtype2                  29
  subtype3                  30
D7V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           12        7       13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        3        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        1        2        0
  CURRENT SMOKER                                        14       18       19
  LIFELONG NON-SMOKER                                   53       29       30
[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
D7V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           2       39             1        0        6
  subtype2           2       18             5        0        4
  subtype3          15       17             9        1        2
D7V21, multiclass
               clus
vv              subtype1 subtype2 subtype3
  COMBINATION          2        2       15
  EXTERNAL            39       18       17
  EXTERNAL BEAM        1        5        9
  IMPLANTS             0        0        1
  INTERNAL             6        4        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"
D7V22, binary
          cls
clus        0  1
  subtype1  3  0
  subtype2  5  0
  subtype3 19  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    5    0
  subtype3   19    3
                         clus
vv                        subtype1 subtype2 subtype3
  COMPLETED AS PLANNED           3        5       19
  TREATMENT NOT COMPLETED        0        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                  12
  subtype2                  1                1                   8
  subtype3                  0                1                   9
          vv
clus       REGIONAL SITE
  subtype1             8
  subtype2             5
  subtype3             3
D7V23, multiclass
                     clus
vv                    subtype1 subtype2 subtype3
  DISTANT RECURRENCE         1        1        0
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD       12        8        9
  REGIONAL SITE              8        5        3
[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"
D7V24, binary
          cls
clus        0  1
  subtype1 17  1
  subtype2  9  1
  subtype3  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    1
  subtype2    9    1
  subtype3    9    1
     clus
vv    subtype1 subtype2 subtype3
  CGY       17        9        9
  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"
D7V25, continuous
D7V26, continuous
D7V27, continuous
D7V28, continuous
D7V29, continuous
D7V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       7
  subtype2                                   1                       8
  subtype3                                   4                      17
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       1
  subtype2                       1                       4
  subtype3                       0                       4
D7V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        4
  OTHER LOCATION, SPECIFY                    7        8       17
  POSITIVE BLADDER MARGIN                    0        1        0
  POSITIVE VAGINAL MARGIN                    1        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"
          vv
clus       INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  subtype1                                             0
  subtype2                                             0
  subtype3                                             2
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              9
  subtype2                                              4
  subtype3                                              3
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                23
  subtype2                                                                                21
  subtype3                                                                                21
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           44
  subtype2                                                                                           27
  subtype3                                                                                           33
D7V32, multiclass
                                                                                              clus
vv                                                                                             subtype1
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      9
  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)       44
                                                                                              clus
vv                                                                                             subtype2
  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)                  21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       27
                                                                                              clus
vv                                                                                             subtype3
  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)                  21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       33
[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"
D7V33, binary
          cls
clus        0  1
  subtype1 23 22
  subtype2 22 21
  subtype3 21 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   22
  subtype2   22   21
  subtype3   21   27
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        23       22       21
  PRESENT       22       21       27
[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"
D7V34, continuous
D7V35, continuous
D7V36, binary
          cls
clus        0  1
  subtype1  8 35
  subtype2 17 25
  subtype3 21 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   35
  subtype2   17   25
  subtype3   21   32
                                          clus
vv                                         subtype1 subtype2 subtype3
  KERATINIZING SQUAMOUS CELL CARCINOMA            8       17       21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       35       25       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"
D7V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          19         26
  subtype2            3          15         14
  subtype3            2          15         18
D7V38, multiclass
              clus
vv             subtype1 subtype2 subtype3
  CURRENT USER        5        3        2
  FORMER USER        19       15       15
  NEVER USED         26       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"
D7V39, continuous
D7V40, binary
          cls
clus        0  1
  subtype1 29  4
  subtype2 28  5
  subtype3 35  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    4
  subtype2   28    5
  subtype3   35    8
         clus
vv        subtype1 subtype2 subtype3
  ABSENT        29       28       35
  PRESENT        4        5        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       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         2     0
  subtype2           0         2     1
  subtype3           3        13     0
D7V41, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        3       16 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2"
             clus
vv            subtype2 subtype3
  CARBOPLATIN        0        3
  CISPLATIN          2       13
  OTHER              1        0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V42, continuous
          vv
clus       T1A T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   1   9   26   10  2   4    2    5  10   4  2   1  8
  subtype2   0   4   21    9  0   4    3    2   4   1  1   0  5
  subtype3   0  18   19    5  2   0    2    2   7   2  1   0  2
D7V43, multiclass
      clus
vv     subtype1 subtype2 subtype3
  T1A         1        0        0
  T1B         9        4       18
  T1B1       26       21       19
  T1B2       10        9        5
  T2          2        0        2
  T2A         4        4        0
  T2A1        2        3        2
  T2A2        5        2        2
  T2B        10        4        7
  T3B         4        1        2
  T4          2        1        1
  TIS         1        0        0
  TX          8        5        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"
D7V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       3        1         0        8        32        14        1
  subtype2       0        1         1        4        22        11        2
  subtype3       1        0         0       22        14         7        1
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIB STAGE IVA
  subtype1         2          0          4        13         13         1
  subtype2         3          3          2         6          6         3
  subtype3         1          2          1         7         14         1
          vv
clus       STAGE IVB
  subtype1         4
  subtype2         1
  subtype3         1
D7V45, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        0        1
  STAGE IA          1        1        0
  STAGE IA2         0        1        0
  STAGE IB          8        4       22
  STAGE IB1        32       22       14
  STAGE IB2        14       11        7
  STAGE II          1        2        1
  STAGE IIA         2        3        1
  STAGE IIA1        0        3        2
  STAGE IIA2        4        2        1
  STAGE IIB        13        6        7
  STAGE IIIB       13        6       14
  STAGE IVA         1        3        1
  STAGE IVB         4        1        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"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 40  9
  subtype2 33  7
  subtype3 19 12
  subtype4 91 24
subtype1 subtype2 subtype3 subtype4 
      49       40       31      115 
subtype1 subtype2 subtype3 subtype4 
       9        7       12       24 
$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-C5-A8YT TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.35         2.73         6.12         1.12        58.88        50.76 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
       16.18        17.52         1.35        14.50        12.82        14.89 
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-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 
        2.17         1.02         1.35         1.32         1.12         9.44 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A69B 
      137.16        66.81        96.95        81.96         3.29        10.06 
TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV 
       30.31         0.20        29.72         2.96        15.58        16.14 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QH 
       15.88         6.25        61.28        19.96        23.28        39.78 
TCGA-VS-A952 
       44.88 

$subtype2
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7XC 
       20.42       101.82       134.33        15.48       147.35        50.99 
TCGA-C5-A8XJ TCGA-C5-A8ZZ TCGA-DG-A2KL TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A3HR 
       75.78        20.91        44.94        16.83         0.76         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZD 
        0.82         0.62         1.35        12.66         0.26        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RC 
       14.99        13.48         0.36         0.59         0.13         4.04 
TCGA-EK-A2RO TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.07         1.45        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A8JM TCGA-Q1-A5R2 
       14.93       147.39         0.89        13.87         5.42        13.35 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8QM 
       93.99        14.07        32.15        31.27 

$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-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        3.58        33.90        87.75        58.88        36.76         2.66 
TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT TCGA-FU-A23K 
       28.90        28.31        12.36       127.36        12.36         1.22 
TCGA-FU-A23L 
       23.84 

$subtype4
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A1MN TCGA-C5-A2LT 
       57.04        11.44        18.74        19.86        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05        78.35       100.14        52.01        18.02 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      182.93       154.32        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ 
        9.34        13.61        45.83         8.35        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A901 TCGA-C5-A902 TCGA-C5-A905 TCGA-C5-A907 TCGA-DG-A2KM 
       27.52        17.03         4.90       160.41         4.47        40.04 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ 
      117.99       118.65         8.75        22.98         8.28         1.74 
TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A43B TCGA-EA-A5FO 
        2.66        13.05         1.18        14.50         1.81         1.48 
TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2IR 
       13.58        12.59        45.96        26.27         6.64       113.16 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RJ 
        1.51         0.43         1.45        16.08         0.07         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        0.10         0.03         6.94        19.79         6.12         4.73 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         0.66         1.58         1.48         0.82         3.52 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
        1.97         9.01       117.40        78.71        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       27.42        24.56        21.44        20.48        15.58         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 
        6.71        21.11         7.99        11.28         0.07         0.30 
TCGA-LP-A5U3 TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.82         0.07         4.34         5.49        15.95         3.39 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       17.56        14.07         5.88        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EK 
       11.67        10.03        34.52        29.03        20.22        27.25 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y 
       53.52        46.03        11.51        49.55        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       23.24        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     1.22     0.03 
subtype1 subtype2 subtype3 subtype4 
  137.16   147.39   177.04   182.93 
subtype1 subtype2 subtype3 subtype4 
   14.96    14.50    35.61    16.08 
[1] "0.1 - 137.2 (15.0)" "0.1 - 147.4 (14.5)" "1.2 - 177.0 (35.6)"
[4] "0.0 - 182.9 (16.1)"
D8V2, continuous
          vv
clus       T1 T2 T3 T4
  subtype1 28 13  0  1
  subtype2 22  7  1  1
  subtype3 20  5  1  0
  subtype4 52 24  5  2
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       28       22       20       52
  T2       13        7        5       24
  T3        0        1        1        5
  T4        1        1        0        2
[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"
D8V4, binary
          cls
clus        0  1
  subtype1 30  8
  subtype2 21  8
  subtype3 13 13
  subtype4 48 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    8
  subtype2   21    8
  subtype3   13   13
  subtype4   48   19
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       30       21       13       48
  1        8        8       13       19
[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 20  4 20
  subtype2 18  1 13
  subtype3 17  0  9
  subtype4 41  2 48
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       20       18       17       41
  M1        4        1        0        2
  MX       20       13        9       48
[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             3                               14
  subtype2             1                               41
  subtype3             0                               30
  subtype4             1                              114
          vv
clus       ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  subtype1                                             4
  subtype2                                             0
  subtype3                                             0
  subtype4                                             1
          vv
clus       ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                  20
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
          vv
clus       ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  subtype1                                         3
  subtype2                                         0
  subtype3                                         0
  subtype4                                         0
          vv
clus       MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  subtype1                                            6
  subtype2                                            0
  subtype3                                            0
  subtype4                                            0
D8V6, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADENOSQUAMOUS                                        3        1        0
  CERVICAL SQUAMOUS CELL CARCINOMA                    14       41       30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        4        0        0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                 20        0        1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            3        0        0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         6        0        0
                                               clus
vv                                              subtype4
  ADENOSQUAMOUS                                        1
  CERVICAL SQUAMOUS CELL CARCINOMA                   114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE        1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                  0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX            0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE         0
[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"
D8V7, binary
          cls
clus         0   1
  subtype1   1  49
  subtype2   3  39
  subtype3  19  12
  subtype4  10 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   49
  subtype2    3   39
  subtype3   19   12
  subtype4   10  106
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        3       19       10
  YES       49       39       12      106
[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"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                1     5                         1
  subtype3                                0     2                         3
  subtype4                                5     6                        16
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    36
  subtype2                                         0    31
  subtype3                                         0    26
  subtype4                                         1    79
D8V10, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        0        5
  ASIAN                                            5        5        2        6
  BLACK OR AFRICAN AMERICAN                        3        1        3       16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           36       31       26       79
[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"
D8V11, binary
          cls
clus        0  1
  subtype1  6 31
  subtype2  1 29
  subtype3  1 22
  subtype4  9 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   31
  subtype2    1   29
  subtype3    1   22
  subtype4    9   66
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            6        1        1        9
  NOT HISPANIC OR LATINO       31       29       22       66
[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"
D8V12, continuous
D8V13, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 11  2
  subtype3 16 10
  subtype4 28 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   11    2
  subtype3   16   10
  subtype4   28   11
            clus
vv           subtype1 subtype2 subtype3 subtype4
  TUMOR FREE       17       11       16       28
  WITH TUMOR        4        2       10       11
[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       BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  subtype1      4      3       1      2       1            36       3
  subtype2      3      1       0      5       2            26       5
  subtype3      0      0       0      1       0            30       0
  subtype4     17      1       0      3       3            87       5
D8V14, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  BRAZIL               4        3        0       17
  CANADA               3        1        0        1
  NIGERIA              1        0        0        0
  RUSSIA               2        5        1        3
  UKRAINE              1        2        0        3
  UNITED STATES       36       26       30       87
  VIETNAM              3        5        0        5
[1] 7 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 22 18  0  4
  subtype2  5 23 11  0  2
  subtype3  0 17 14  0  0
  subtype4  4 44 57  1  8
D8V15, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  G1        6        5        0        4
  G2       22       23       17       44
  G3       18       11       14       57
  G4        0        0        0        1
  GX        4        2        0        8
[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"
D8V16, continuous
D8V17, continuous
          vv
clus       CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  subtype1                                           5
  subtype2                                           3
  subtype3                                           8
  subtype4                                          16
          vv
clus       CURRENT REFORMED SMOKER FOR > 15 YEARS
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
  subtype4                                      2
          vv
clus       CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER
  subtype1                                               0              9
  subtype2                                               1             10
  subtype3                                               0              5
  subtype4                                               2             27
          vv
clus       LIFELONG NON-SMOKER
  subtype1                  29
  subtype2                  19
  subtype3                  14
  subtype4                  50
D8V18, multiclass
                                                 clus
vv                                                subtype1 subtype2 subtype3
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS            5        3        8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 1        2        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        0        1        0
  CURRENT SMOKER                                         9       10        5
  LIFELONG NON-SMOKER                                   29       19       14
                                                 clus
vv                                                subtype4
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS           16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                 2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED        2
  CURRENT SMOKER                                        27
  LIFELONG NON-SMOKER                                   50
[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"
D8V19, continuous
D8V20, continuous
          vv
clus       COMBINATION EXTERNAL EXTERNAL BEAM IMPLANTS INTERNAL
  subtype1           1       17             0        0        1
  subtype2           0       11             3        0        3
  subtype3          13        1             7        1        0
  subtype4           5       45             5        0        8
D8V21, multiclass
               clus
vv              subtype1 subtype2 subtype3 subtype4
  COMBINATION          1        0       13        5
  EXTERNAL            17       11        1       45
  EXTERNAL BEAM        0        3        7        5
  IMPLANTS             0        0        1        0
  INTERNAL             1        3        0        8
[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"
D8V22, binary
          cls
clus        0  1
  subtype1  1  0
  subtype2  2  0
  subtype3 17  1
  subtype4  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    0
  subtype2    2    0
  subtype3   17    1
  subtype4    7    2
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  COMPLETED AS PLANNED           1        2       17        7
  TREATMENT NOT COMPLETED        0        0        1        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"
          vv
clus       DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  subtype1                  1                0                   3
  subtype2                  0                1                   5
  subtype3                  0                0                   2
  subtype4                  1                1                  19
          vv
clus       REGIONAL SITE
  subtype1             1
  subtype2             4
  subtype3             0
  subtype4            11
D8V23, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5       10        2       32 
 [1] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype2" "subtype4" "subtype4" "subtype1" "subtype2" "subtype4"
[19] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype2"
[25] "subtype1" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype2"
[37] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype4"
[43] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
                     clus
vv                    subtype1 subtype2 subtype4
  DISTANT RECURRENCE         1        0        1
  LOCAL RECURRENCE           0        1        1
  PRIMARY TUMOR FIELD        3        5       19
  REGIONAL SITE              1        4       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"
D8V24, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2  6  1
  subtype3  2  0
  subtype4 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    6    1
  subtype3    2    0
  subtype4   22    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  CGY        5        6        2       22
  GY         0        1        0        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"
D8V25, continuous
D8V26, continuous
D8V27, continuous
D8V28, continuous
D8V29, continuous
D8V30, continuous
          vv
clus       MACROSCOPIC PARAMETRIAL INVOLVEMENT
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
          vv
clus       MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  subtype1                                   1                       5
  subtype2                                   1                       4
  subtype3                                   2                      13
  subtype4                                   2                      10
          vv
clus       POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  subtype1                       0                       2
  subtype2                       1                       1
  subtype3                       0                       2
  subtype4                       0                       4
D8V31, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  MACROSCOPIC PARAMETRIAL INVOLVEMENT        0        1        0        0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT        1        1        2        2
  OTHER LOCATION, SPECIFY                    5        4       13       10
  POSITIVE BLADDER MARGIN                    0        1        0        0
  POSITIVE VAGINAL MARGIN                    2        1        2        4
[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                                             0
  subtype2                                             0
  subtype3                                             2
  subtype4                                             0
          vv
clus       PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  subtype1                                              3
  subtype2                                              3
  subtype3                                              1
  subtype4                                              9
          vv
clus       POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  subtype1                                                                                14
  subtype2                                                                                13
  subtype3                                                                                12
  subtype4                                                                                26
          vv
clus       PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  subtype1                                                                                           25
  subtype2                                                                                           16
  subtype3                                                                                           14
  subtype4                                                                                           49
D8V32, 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)                  14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       25
                                                                                              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)                  13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       16
                                                                                              clus
vv                                                                                             subtype3
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       2
  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)       14
                                                                                              clus
vv                                                                                             subtype4
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                       0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                      9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                  26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)       49
[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"
D8V33, binary
          cls
clus        0  1
  subtype1 20 15
  subtype2 13 13
  subtype3  6 18
  subtype4 27 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   15
  subtype2   13   13
  subtype3    6   18
  subtype4   27   24
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        20       13        6       27
  PRESENT       15       13       18       24
[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"
D8V34, continuous
D8V35, continuous
D8V36, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2 13 15
  subtype3  9 12
  subtype4 24 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2   13   15
  subtype3    9   12
  subtype4   24   54
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  KERATINIZING SQUAMOUS CELL CARCINOMA            0       13        9       24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA       11       15       12       54
[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"
D8V37, continuous
          vv
clus       CURRENT USER FORMER USER NEVER USED
  subtype1            5          13         12
  subtype2            0           9          9
  subtype3            0           5         10
  subtype4            5          22         27
D8V38, multiclass
              clus
vv             subtype1 subtype2 subtype3 subtype4
  CURRENT USER        5        0        0        5
  FORMER USER        13        9        5       22
  NEVER USED         12        9       10       27
[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"
D8V39, continuous
D8V40, binary
          cls
clus        0  1
  subtype1 27  4
  subtype2 16  3
  subtype3 17  6
  subtype4 32  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    4
  subtype2   16    3
  subtype3   17    6
  subtype4   32    4
         clus
vv        subtype1 subtype2 subtype3 subtype4
  ABSENT        27       16       17       32
  PRESENT        4        3        6        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"
          vv
clus       CARBOPLATIN CISPLATIN OTHER
  subtype1           0         0     0
  subtype2           0         1     0
  subtype3           3         9     0
  subtype4           0         7     1
D8V41, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 subtype4 
       1       12        8 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
[19] "subtype4" "subtype4"
             clus
vv            subtype3 subtype4
  CARBOPLATIN        3        0
  CISPLATIN          9        7
  OTHER              0        1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V42, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        4        3        4 
 [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype2" "subtype4"
 [7] "subtype2" "subtype4" "subtype2" "subtype2" "subtype4"
          vv
clus       T1A T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TIS TX
  subtype1   0   3   20    5  1   2    2    3   5   0  1   0  2
  subtype2   0   6   12    4  0   3    1    1   2   1  1   0  2
  subtype3   0   8    9    3  1   0    1    0   3   1  0   0  0
  subtype4   1  14   25   12  2   3    3    5  11   5  2   1 11
D8V43, multiclass
      clus
vv     subtype1 subtype2 subtype3 subtype4
  T1A         0        0        0        1
  T1B         3        6        8       14
  T1B1       20       12        9       25
  T1B2        5        4        3       12
  T2          1        0        1        2
  T2A         2        3        0        3
  T2A1        2        1        1        3
  T2A2        3        1        0        5
  T2B         5        2        3       11
  T3B         0        1        1        5
  T4          1        1        0        2
  TIS         0        0        0        1
  TX          2        2        0       11
[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"
D8V44, continuous
          vv
clus       STAGE I STAGE IA STAGE IA2 STAGE IB STAGE IB1 STAGE IB2 STAGE II
  subtype1       1        0         0        3        22         8        1
  subtype2       0        1         1        4        14         4        1
  subtype3       0        0         0       12         5         4        0
  subtype4       3        1         0       15        27        16        2
          vv
clus       STAGE IIA STAGE IIA1 STAGE IIA2 STAGE IIB STAGE IIIB STAGE IVA
  subtype1         1          1          2         4          4         0
  subtype2         2          1          1         5          4         2
  subtype3         1          1          0         2          6         0
  subtype4         2          2          4        15         19         3
          vv
clus       STAGE IVB
  subtype1         3
  subtype2         1
  subtype3         0
  subtype4         2
D8V45, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        0        0        3
  STAGE IA          0        1        0        1
  STAGE IA2         0        1        0        0
  STAGE IB          3        4       12       15
  STAGE IB1        22       14        5       27
  STAGE IB2         8        4        4       16
  STAGE II          1        1        0        2
  STAGE IIA         1        2        1        2
  STAGE IIA1        1        1        1        2
  STAGE IIA2        2        1        0        4
  STAGE IIB         4        5        2       15
  STAGE IIIB        4        4        6       19
  STAGE IVA         0        2        0        3
  STAGE IVB         3        1        0        2
[1] 14  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
