[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"        "-oTPRAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/11541653/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/10695255/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=261, common to both=256
[1] "Reduce the number of clustering variables from 41 to 37."
[1]  37 256
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            26            230 
  SPOP MUTATED SPOP WILD-TYPE 
            26            230 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            22            234 
  TP53 MUTATED TP53 WILD-TYPE 
            22            234 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            12            244 
  PTEN MUTATED PTEN WILD-TYPE 
            12            244 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              247 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              247 
[1] "TCEB3 MUTATION ANALYSIS"
[1] 3
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             252 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             252 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             244 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             244 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             5            251 
  BRAF MUTATED BRAF WILD-TYPE 
             5            251 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9              247 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9              247 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            252 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            252 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               8              248 
  FAM47C MUTATED FAM47C WILD-TYPE 
               8              248 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                5               251 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                5               251 
[1] "CNTNAP1 MUTATION ANALYSIS"
[1] 3
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                5               251 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                5               251 
[1] "MLLT10 MUTATION ANALYSIS"
[1] 3
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              252 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              252 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              5             251 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              5             251 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
             4            252 
  SMG7 MUTATED SMG7 WILD-TYPE 
             4            252 
[1] "EDC4 MUTATION ANALYSIS"
[1] 3
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            253 
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            253 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              252 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               4              252 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              7             249 
  CDK12 MUTATED CDK12 WILD-TYPE 
              7             249 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             6            250 
  RPTN MUTATED RPTN WILD-TYPE 
             6            250 
[1] "TNRC18 MUTATION ANALYSIS"
[1] 3
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              252 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              252 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
              5             251 
  MED15 MUTATED MED15 WILD-TYPE 
              5             251 
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              251 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              251 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             250 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             250 
[1] "RNF31 MUTATION ANALYSIS"
[1] 3
  RNF31 MUTATED RNF31 WILD-TYPE 
              4             252 
  RNF31 MUTATED RNF31 WILD-TYPE 
              4             252 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             252 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             252 
[1] "LMOD2 MUTATION ANALYSIS"
[1] 3
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             253 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             253 
[1] "FAM120B MUTATION ANALYSIS"
[1] 3
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               253 
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               253 
[1] "CLEC1A MUTATION ANALYSIS"
[1] 3
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               4              252 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               4              252 
[1] "RNF17 MUTATION ANALYSIS"
[1] 3
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             253 
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             253 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              7             249 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              7             249 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              4             252 
  EOMES MUTATED EOMES WILD-TYPE 
              4             252 
[1] "MTF1 MUTATION ANALYSIS"
[1] 3
  MTF1 MUTATED MTF1 WILD-TYPE 
             3            253 
  MTF1 MUTATED MTF1 WILD-TYPE 
             3            253 
[1] "NTM MUTATION ANALYSIS"
[1] 3
  NTM MUTATED NTM WILD-TYPE 
            5           251 
  NTM MUTATED NTM WILD-TYPE 
            5           251 
[1] "FNBP4 MUTATION ANALYSIS"
[1] 3
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              3             253 
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              3             253 
[1] "CDKN1B MUTATION ANALYSIS"
[1] 3
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              252 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              252 
[1] "EIF2AK3 MUTATION ANALYSIS"
[1] 3
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4               252 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4               252 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              3             253 
  LARP1 MUTATED LARP1 WILD-TYPE 
              3             253 
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCHNUMBER"                           

Input Data has 29 rows and 256 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          425 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
          60           91          731           31          396         1065 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
         943           31           62           28         1339          365 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
          31          700           31          458          731           62 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
         396          486          821          304          974         1004 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
          91          882          826         1007          595          405 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
         906         1415         1365          800         1391          880 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
         922          827          727         1184         1464         1116 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
        1476         1172         1102         1832         1416         1454 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
        1590         1962         1578         2079         1310         1115 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
        1179         1209         1832         1273         1456          884 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
         822         1491         1860          295          289          285 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
         233          175          842          191            9          727 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        1167          787          781          625          442          430 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
         552          596          526          114          701          606 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
        1961         1946          821           NA          314          162 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
         129          532          299           93          229          668 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
         536          393          417          560          278           91 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
         230          864          469          409          273          524 
TCGA-FC-A6HD TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
         494         1266         2657         2465         2068         2028 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
        2110         1696          554         2089         1515         1404 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
        1542         1501         1434         1415         1443         1378 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
        1198         1363          101         1222         1215         1156 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
        1226          811          958         1155         1393          765 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
         830         1771         1726         1608         1543         1185 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
         849          942         1075          857          994          185 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
         941          112          601           NA          162           89 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
          61           72          440          868           24          870 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
          60           51           72           89           52           22 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
          64           81           53           45           51           63 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
         748          792           60           34           98          928 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
          45          543          747           56          589          682 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
          95          726           66           69           59          546 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
         679           48          483           35          680           23 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
          54           61           67           49          167           71 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
         106           44           38          134         2391         2684 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
        2522           NA          614          374          662          518 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
         488          503          491          624          454          523 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J9-A52B TCGA-J9-A52C 
         183          405          528          279          422          178 
TCGA-J9-A52D TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
         212          323         2859         1712         1359         1879 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
        2364         3524          913         1659         4604         2056 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-QU-A6IL 
        2753         1498         3447         2040         1770           97 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        1247         3487         1436         2620 
Variable 1:'AGE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=230,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=139,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=133,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 25:'PSA_VALUE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=197,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "HISTOLOGICAL.TYPE"        
 [5] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 256 columns, 0 survival variables, and 13 non-survival variables.
AGE, nv=32, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
115 134   5 
[1] "table(vv)"
vv
 T2  T3  T4 
115 134   5 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T2  T3  T4 
115 134   5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
115 134   5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=139, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=57, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SPOP MUTATION ANALYSIS
D1V1, continuous
                vv
clus              T2  T3  T4
  SPOP MUTATED    13  13   0
  SPOP WILD-TYPE 102 121   5
D1V2, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  T2           13            102
  T3           13            121
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V3, binary
                cls
clus               0   1
  SPOP MUTATED    21   2
  SPOP WILD-TYPE 169  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     21    2
  SPOP WILD-TYPE  169   21
   clus
vv  SPOP MUTATED SPOP WILD-TYPE
  0           21            169
  1            2             21
[1] 2 2
[1] FALSE
D1V4, binary
                cls
clus               0   1
  SPOP MUTATED     2  24
  SPOP WILD-TYPE   4 226
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      2   24
  SPOP WILD-TYPE    4  226
                                        clus
vv                                       SPOP MUTATED SPOP WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            2              4
  PROSTATE ADENOCARCINOMA ACINAR TYPE              24            226
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    18   4   0   1
  SPOP WILD-TYPE 163  48   2   7
D1V5, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           18            163
  R1            4             48
  R2            0              2
  RX            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, continuous
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPOP MUTATED       0                         1    12
  SPOP WILD-TYPE     2                         6   135
D1V13, multiclass
                           clus
vv                          SPOP MUTATED SPOP WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                               12            135
[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"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, continuous
                vv
clus              T2  T3  T4
  TP53 MUTATED     7  15   0
  TP53 WILD-TYPE 108 119   5
D2V2, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T2            7            108
  T3           15            119
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V3, binary
                cls
clus               0   1
  TP53 MUTATED    19   3
  TP53 WILD-TYPE 171  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19    3
  TP53 WILD-TYPE  171   20
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           19            171
  1            3             20
[1] 2 2
[1] FALSE
D2V4, binary
                cls
clus               0   1
  TP53 MUTATED     0  22
  TP53 WILD-TYPE   6 228
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   22
  TP53 WILD-TYPE    6  228
                                        clus
vv                                       TP53 MUTATED TP53 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE              22            228
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    16   6   0   0
  TP53 WILD-TYPE 165  46   2   8
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           16            165
  R1            6             46
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, continuous
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0    12
  TP53 WILD-TYPE     2                         7   135
D2V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                               12            135
[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"

Clustering(3) Variable = PTEN MUTATION ANALYSIS
D3V1, continuous
                vv
clus              T2  T3  T4
  PTEN MUTATED     6   6   0
  PTEN WILD-TYPE 109 128   5
D3V2, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T2            6            109
  T3            6            128
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V3, binary
                cls
clus               0   1
  PTEN MUTATED     9   2
  PTEN WILD-TYPE 181  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      9    2
  PTEN WILD-TYPE  181   21
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            9            181
  1            2             21
[1] 2 2
[1] FALSE
D3V4, binary
                cls
clus               0   1
  PTEN MUTATED     1  11
  PTEN WILD-TYPE   5 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   11
  PTEN WILD-TYPE    5  239
                                        clus
vv                                       PTEN MUTATED PTEN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              5
  PROSTATE ADENOCARCINOMA ACINAR TYPE              11            239
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     7   2   0   1
  PTEN WILD-TYPE 174  50   2   7
D3V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            7            174
  R1            2             50
  R2            0              2
  RX            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, continuous
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0     8
  PTEN WILD-TYPE     2                         7   139
D3V13, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                8            139
[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"

Clustering(4) Variable = CTNNB1 MUTATION ANALYSIS
D4V1, continuous
                  vv
clus                T2  T3  T4
  CTNNB1 MUTATED     6   3   0
  CTNNB1 WILD-TYPE 109 131   5
D4V2, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T2              6              109
  T3              3              131
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V3, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     8   0
  CTNNB1 WILD-TYPE 182  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      8    0
  CTNNB1 WILD-TYPE  182   23
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0              8              182
  1              0               23
[1] 2 2
[1] FALSE
D4V4, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     1   8
  CTNNB1 WILD-TYPE   5 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1    8
  CTNNB1 WILD-TYPE    5  242
                                        clus
vv                                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1                5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 8              242
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED     7   1   0   0
  CTNNB1 WILD-TYPE 174  51   2   8
D4V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              7              174
  R1              1               51
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, continuous
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED       0                         0     5
  CTNNB1 WILD-TYPE     2                         7   142
D4V13, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[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"

Clustering(5) Variable = TCEB3 MUTATION ANALYSIS
D5V1, continuous
                 vv
clus               T2  T3  T4
  TCEB3 MUTATED     1   3   0
  TCEB3 WILD-TYPE 114 131   5
D5V2, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  T2             1             114
  T3             3             131
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V3, binary
                 cls
clus                0   1
  TCEB3 MUTATED     2   1
  TCEB3 WILD-TYPE 188  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      2    1
  TCEB3 WILD-TYPE  188   22
   clus
vv  TCEB3 MUTATED TCEB3 WILD-TYPE
  0             2             188
  1             1              22
[1] 2 2
[1] FALSE
D5V4, binary
                 cls
clus                0   1
  TCEB3 MUTATED     0   4
  TCEB3 WILD-TYPE   6 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      0    4
  TCEB3 WILD-TYPE    6  246
                                        clus
vv                                       TCEB3 MUTATED TCEB3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             246
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TCEB3 MUTATED     3   1   0   0
  TCEB3 WILD-TYPE 178  51   2   8
D5V5, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  R0             3             178
  R1             1              51
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, continuous
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCEB3 MUTATED       0                         0     2
  TCEB3 WILD-TYPE     2                         7   145
D5V13, multiclass
[1] "Remove cluster labels:" "TCEB3 MUTATED"         
clus
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 

Clustering(6) Variable = FOXA1 MUTATION ANALYSIS
D6V1, continuous
                 vv
clus               T2  T3  T4
  FOXA1 MUTATED     8   4   0
  FOXA1 WILD-TYPE 107 130   5
D6V2, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  T2             8             107
  T3             4             130
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V3, binary
                 cls
clus                0   1
  FOXA1 MUTATED     9   0
  FOXA1 WILD-TYPE 181  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      9    0
  FOXA1 WILD-TYPE  181   23
   clus
vv  FOXA1 MUTATED FOXA1 WILD-TYPE
  0             9             181
  1             0              23
[1] 2 2
[1] FALSE
D6V4, binary
                 cls
clus                0   1
  FOXA1 MUTATED     0  12
  FOXA1 WILD-TYPE   6 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      0   12
  FOXA1 WILD-TYPE    6  238
                                        clus
vv                                       FOXA1 MUTATED FOXA1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               12             238
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXA1 MUTATED     9   2   0   1
  FOXA1 WILD-TYPE 172  50   2   7
D6V5, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  R0             9             172
  R1             2              50
  R2             0               2
  RX             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, continuous
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXA1 MUTATED       0                         2     5
  FOXA1 WILD-TYPE     2                         5   142
D6V13, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               5
  WHITE                                 5             142
[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"

Clustering(7) Variable = BRAF MUTATION ANALYSIS
D7V1, continuous
                vv
clus              T2  T3  T4
  BRAF MUTATED     1   4   0
  BRAF WILD-TYPE 114 130   5
D7V2, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T2            1            114
  T3            4            130
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V3, binary
                cls
clus               0   1
  BRAF MUTATED     4   0
  BRAF WILD-TYPE 186  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      4    0
  BRAF WILD-TYPE  186   23
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0            4            186
  1            0             23
[1] 2 2
[1] FALSE
D7V4, binary
                cls
clus               0   1
  BRAF MUTATED     1   4
  BRAF WILD-TYPE   5 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1    4
  BRAF WILD-TYPE    5  246
                                        clus
vv                                       BRAF MUTATED BRAF WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              5
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            246
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED     4   1   0   0
  BRAF WILD-TYPE 177  51   2   8
D7V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0            4            177
  R1            1             51
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, continuous
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       0                         0     2
  BRAF WILD-TYPE     2                         7   145
D7V13, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7314 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7231     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7744 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818     TCGA-HC-7819 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 

Clustering(8) Variable = PIK3CA MUTATION ANALYSIS
D8V1, continuous
                  vv
clus                T2  T3  T4
  PIK3CA MUTATED     3   6   0
  PIK3CA WILD-TYPE 112 128   5
D8V2, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T2              3              112
  T3              6              128
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     6   1
  PIK3CA WILD-TYPE 184  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      6    1
  PIK3CA WILD-TYPE  184   22
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              6              184
  1              1               22
[1] 2 2
[1] FALSE
D8V4, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1   8
  PIK3CA WILD-TYPE   5 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    8
  PIK3CA WILD-TYPE    5  242
                                        clus
vv                                       PIK3CA MUTATED PIK3CA WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1                5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 8              242
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED     6   1   1   1
  PIK3CA WILD-TYPE 175  51   1   7
D8V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0              6              175
  R1              1               51
  R2              1                1
  RX              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, continuous
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         0     5
  PIK3CA WILD-TYPE     2                         7   142
D8V13, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[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"

Clustering(9) Variable = IDH1 MUTATION ANALYSIS
D9V1, continuous
                vv
clus              T2  T3  T4
  IDH1 MUTATED     1   3   0
  IDH1 WILD-TYPE 114 131   5
D9V2, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T2            1            114
  T3            3            131
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V3, binary
                cls
clus               0   1
  IDH1 MUTATED     3   1
  IDH1 WILD-TYPE 187  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3    1
  IDH1 WILD-TYPE  187   22
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            3            187
  1            1             22
[1] 2 2
[1] FALSE
D9V4, binary
                cls
clus               0   1
  IDH1 MUTATED     0   4
  IDH1 WILD-TYPE   6 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0    4
  IDH1 WILD-TYPE    6  246
                                        clus
vv                                       IDH1 MUTATED IDH1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            246
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED     1   3   0   0
  IDH1 WILD-TYPE 180  49   2   8
D9V5, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0            1            180
  R1            3             49
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, continuous
D9V7, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0     2
  IDH1 WILD-TYPE     2                         7   145
D9V13, multiclass
[1] "Remove cluster labels:" "IDH1 MUTATED"          
clus
  IDH1 MUTATED IDH1 WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7314     TCGA-EJ-7315 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332     TCGA-G9-6333 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342     TCGA-G9-6343 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818     TCGA-HC-7819 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 

Clustering(10) Variable = FAM47C MUTATION ANALYSIS
D10V1, continuous
                  vv
clus                T2  T3  T4
  FAM47C MUTATED     4   4   0
  FAM47C WILD-TYPE 111 130   5
D10V2, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  T2              4              111
  T3              4              130
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V3, binary
                  cls
clus                 0   1
  FAM47C MUTATED     6   0
  FAM47C WILD-TYPE 184  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      6    0
  FAM47C WILD-TYPE  184   23
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0              6              184
  1              0               23
[1] 2 2
[1] FALSE
D10V4, binary
                  cls
clus                 0   1
  FAM47C MUTATED     0   8
  FAM47C WILD-TYPE   6 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      0    8
  FAM47C WILD-TYPE    6  242
                                        clus
vv                                       FAM47C MUTATED FAM47C WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 8              242
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM47C MUTATED     7   1   0   0
  FAM47C WILD-TYPE 174  51   2   8
D10V5, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  R0              7              174
  R1              1               51
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, continuous
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       0                         0     3
  FAM47C WILD-TYPE     2                         7   144
D10V13, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[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"

Clustering(11) Variable = TP53BP1 MUTATION ANALYSIS
D11V1, continuous
                   vv
clus                 T2  T3  T4
  TP53BP1 MUTATED     1   4   0
  TP53BP1 WILD-TYPE 114 130   5
D11V2, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  T2               1               114
  T3               4               130
  T4               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V3, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     3   0
  TP53BP1 WILD-TYPE 187  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      3    0
  TP53BP1 WILD-TYPE  187   23
   clus
vv  TP53BP1 MUTATED TP53BP1 WILD-TYPE
  0               3               187
  1               0                23
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     0   5
  TP53BP1 WILD-TYPE   6 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      0    5
  TP53BP1 WILD-TYPE    6  245
                                        clus
vv                                       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                 6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               245
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TP53BP1 MUTATED     4   1   0   0
  TP53BP1 WILD-TYPE 177  51   2   8
D11V5, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  R0               4               177
  R1               1                51
  R2               0                 2
  RX               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, continuous
D11V7, continuous
D11V8, continuous
D11V9, continuous
D11V10, continuous
D11V11, continuous
D11V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53BP1 MUTATED       0                         0     2
  TP53BP1 WILD-TYPE     2                         7   145
D11V13, multiclass
[1] "Remove cluster labels:" "TP53BP1 MUTATED"       
clus
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                2               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6342        TCGA-G9-6343 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 

Clustering(12) Variable = CNTNAP1 MUTATION ANALYSIS
D12V1, continuous
                   vv
clus                 T2  T3  T4
  CNTNAP1 MUTATED     2   3   0
  CNTNAP1 WILD-TYPE 113 131   5
D12V2, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  T2               2               113
  T3               3               131
  T4               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V3, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     3   0
  CNTNAP1 WILD-TYPE 187  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      3    0
  CNTNAP1 WILD-TYPE  187   23
   clus
vv  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  0               3               187
  1               0                23
[1] 2 2
[1] FALSE
D12V4, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     1   4
  CNTNAP1 WILD-TYPE   5 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      1    4
  CNTNAP1 WILD-TYPE    5  246
                                        clus
vv                                       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                 5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               246
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CNTNAP1 MUTATED     2   2   0   0
  CNTNAP1 WILD-TYPE 179  50   2   8
D12V5, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  R0               2               179
  R1               2                50
  R2               0                 2
  RX               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, continuous
D12V7, continuous
D12V8, continuous
D12V9, continuous
D12V10, continuous
D12V11, continuous
D12V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP1 MUTATED       0                         0     0
  CNTNAP1 WILD-TYPE     2                         7   147
D12V13, multiclass

Clustering(13) Variable = MLLT10 MUTATION ANALYSIS
D13V1, continuous
                  vv
clus                T2  T3  T4
  MLLT10 MUTATED     2   2   0
  MLLT10 WILD-TYPE 113 132   5
D13V2, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  T2              2              113
  T3              2              132
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V3, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     4   0
  MLLT10 WILD-TYPE 186  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      4    0
  MLLT10 WILD-TYPE  186   23
   clus
vv  MLLT10 MUTATED MLLT10 WILD-TYPE
  0              4              186
  1              0               23
[1] 2 2
[1] FALSE
D13V4, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     0   4
  MLLT10 WILD-TYPE   6 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      0    4
  MLLT10 WILD-TYPE    6  246
                                        clus
vv                                       MLLT10 MUTATED MLLT10 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              246
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MLLT10 MUTATED     4   0   0   0
  MLLT10 WILD-TYPE 177  52   2   8
D13V5, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  R0              4              177
  R1              0               52
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, continuous
D13V7, continuous
D13V8, continuous
D13V9, continuous
D13V10, continuous
D13V11, continuous
D13V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLLT10 MUTATED       0                         0     4
  MLLT10 WILD-TYPE     2                         7   143
D13V13, multiclass
                           clus
vv                          MLLT10 MUTATED MLLT10 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  4              143
[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"

Clustering(14) Variable = ZMYM3 MUTATION ANALYSIS
D14V1, continuous
                 vv
clus               T2  T3  T4
  ZMYM3 MUTATED     1   4   0
  ZMYM3 WILD-TYPE 114 130   5
D14V2, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T2             1             114
  T3             4             130
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V3, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     4   1
  ZMYM3 WILD-TYPE 186  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      4    1
  ZMYM3 WILD-TYPE  186   22
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0             4             186
  1             1              22
[1] 2 2
[1] FALSE
D14V4, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     0   5
  ZMYM3 WILD-TYPE   6 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      0    5
  ZMYM3 WILD-TYPE    6  245
                                        clus
vv                                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             245
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM3 MUTATED     2   3   0   0
  ZMYM3 WILD-TYPE 179  49   2   8
D14V5, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  R0             2             179
  R1             3              49
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, continuous
D14V7, continuous
D14V8, continuous
D14V9, continuous
D14V10, continuous
D14V11, continuous
D14V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM3 MUTATED       0                         0     3
  ZMYM3 WILD-TYPE     2                         7   144
D14V13, multiclass
                           clus
vv                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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"

Clustering(15) Variable = SMG7 MUTATION ANALYSIS
D15V1, continuous
                vv
clus              T2  T3  T4
  SMG7 MUTATED     1   3   0
  SMG7 WILD-TYPE 114 131   5
D15V2, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  T2            1            114
  T3            3            131
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V3, binary
                cls
clus               0   1
  SMG7 MUTATED     4   0
  SMG7 WILD-TYPE 186  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      4    0
  SMG7 WILD-TYPE  186   23
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            4            186
  1            0             23
[1] 2 2
[1] FALSE
D15V4, binary
                cls
clus               0   1
  SMG7 MUTATED     0   4
  SMG7 WILD-TYPE   6 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      0    4
  SMG7 WILD-TYPE    6  246
                                        clus
vv                                       SMG7 MUTATED SMG7 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            246
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMG7 MUTATED     3   1   0   0
  SMG7 WILD-TYPE 178  51   2   8
D15V5, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  R0            3            178
  R1            1             51
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, continuous
D15V7, continuous
D15V8, continuous
D15V9, continuous
D15V10, continuous
D15V11, continuous
D15V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMG7 MUTATED       0                         0     3
  SMG7 WILD-TYPE     2                         7   144
D15V13, multiclass
                           clus
vv                          SMG7 MUTATED SMG7 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            144
[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"

Clustering(16) Variable = EDC4 MUTATION ANALYSIS
D16V1, continuous
                vv
clus              T2  T3  T4
  EDC4 MUTATED     1   2   0
  EDC4 WILD-TYPE 114 132   5
D16V2, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  T2            1            114
  T3            2            132
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V3, binary
                cls
clus               0   1
  EDC4 MUTATED     2   1
  EDC4 WILD-TYPE 188  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      2    1
  EDC4 WILD-TYPE  188   22
   clus
vv  EDC4 MUTATED EDC4 WILD-TYPE
  0            2            188
  1            1             22
[1] 2 2
[1] FALSE
D16V4, binary
                cls
clus               0   1
  EDC4 MUTATED     0   3
  EDC4 WILD-TYPE   6 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      0    3
  EDC4 WILD-TYPE    6  247
                                        clus
vv                                       EDC4 MUTATED EDC4 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            247
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EDC4 MUTATED     3   0   0   0
  EDC4 WILD-TYPE 178  52   2   8
D16V5, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  R0            3            178
  R1            0             52
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, continuous
D16V7, continuous
D16V8, continuous
D16V9, continuous
D16V10, continuous
D16V11, continuous
D16V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDC4 MUTATED       0                         1     2
  EDC4 WILD-TYPE     2                         6   145
D16V13, multiclass
                           clus
vv                          EDC4 MUTATED EDC4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                                2            145
[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"

Clustering(17) Variable = ZNF709 MUTATION ANALYSIS
D17V1, continuous
                  vv
clus                T2  T3  T4
  ZNF709 MUTATED     0   4   0
  ZNF709 WILD-TYPE 115 130   5
D17V2, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  T2              0              115
  T3              4              130
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V3, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     4   0
  ZNF709 WILD-TYPE 186  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      4    0
  ZNF709 WILD-TYPE  186   23
   clus
vv  ZNF709 MUTATED ZNF709 WILD-TYPE
  0              4              186
  1              0               23
[1] 2 2
[1] FALSE
D17V4, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     0   4
  ZNF709 WILD-TYPE   6 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    4
  ZNF709 WILD-TYPE    6  246
                                        clus
vv                                       ZNF709 MUTATED ZNF709 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              246
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF709 MUTATED     2   1   0   1
  ZNF709 WILD-TYPE 179  51   2   7
D17V5, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  R0              2              179
  R1              1               51
  R2              0                2
  RX              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, continuous
D17V7, continuous
D17V8, continuous
D17V9, continuous
D17V10, continuous
D17V11, continuous
D17V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF709 MUTATED       0                         0     2
  ZNF709 WILD-TYPE     2                         7   145
D17V13, multiclass
[1] "Remove cluster labels:" "ZNF709 MUTATED"        
clus
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7330       TCGA-EJ-7331       TCGA-EJ-7781 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 

Clustering(18) Variable = CDK12 MUTATION ANALYSIS
D18V1, continuous
                 vv
clus               T2  T3  T4
  CDK12 MUTATED     3   4   0
  CDK12 WILD-TYPE 112 130   5
D18V2, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T2             3             112
  T3             4             130
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V3, binary
                 cls
clus                0   1
  CDK12 MUTATED     5   1
  CDK12 WILD-TYPE 185  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      5    1
  CDK12 WILD-TYPE  185   22
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0             5             185
  1             1              22
[1] 2 2
[1] FALSE
D18V4, binary
                 cls
clus                0   1
  CDK12 MUTATED     1   6
  CDK12 WILD-TYPE   5 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      1    6
  CDK12 WILD-TYPE    5  244
                                        clus
vv                                       CDK12 MUTATED CDK12 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1               5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             244
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED     4   3   0   0
  CDK12 WILD-TYPE 177  49   2   8
D18V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0             4             177
  R1             3              49
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, continuous
D18V7, continuous
D18V8, continuous
D18V9, continuous
D18V10, continuous
D18V11, continuous
D18V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED       0                         0     1
  CDK12 WILD-TYPE     2                         7   146
D18V13, multiclass
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7785 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 

Clustering(19) Variable = RPTN MUTATION ANALYSIS
D19V1, continuous
                vv
clus              T2  T3  T4
  RPTN MUTATED     4   2   0
  RPTN WILD-TYPE 111 132   5
D19V2, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T2            4            111
  T3            2            132
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V3, binary
                cls
clus               0   1
  RPTN MUTATED     5   0
  RPTN WILD-TYPE 185  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      5    0
  RPTN WILD-TYPE  185   23
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            5            185
  1            0             23
[1] 2 2
[1] FALSE
D19V4, binary
                cls
clus               0   1
  RPTN MUTATED     0   6
  RPTN WILD-TYPE   6 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0    6
  RPTN WILD-TYPE    6  244
                                        clus
vv                                       RPTN MUTATED RPTN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               6            244
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPTN MUTATED     4   0   0   1
  RPTN WILD-TYPE 177  52   2   7
D19V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            4            177
  R1            0             52
  R2            0              2
  RX            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, continuous
D19V7, continuous
D19V8, continuous
D19V9, continuous
D19V10, continuous
D19V11, continuous
D19V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         1     2
  RPTN WILD-TYPE     2                         6   145
D19V13, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                                2            145
[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"

Clustering(20) Variable = TNRC18 MUTATION ANALYSIS
D20V1, continuous
                  vv
clus                T2  T3  T4
  TNRC18 MUTATED     1   3   0
  TNRC18 WILD-TYPE 114 131   5
D20V2, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  T2              1              114
  T3              3              131
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V3, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     3   1
  TNRC18 WILD-TYPE 187  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      3    1
  TNRC18 WILD-TYPE  187   22
   clus
vv  TNRC18 MUTATED TNRC18 WILD-TYPE
  0              3              187
  1              1               22
[1] 2 2
[1] FALSE
D20V4, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     0   4
  TNRC18 WILD-TYPE   6 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      0    4
  TNRC18 WILD-TYPE    6  246
                                        clus
vv                                       TNRC18 MUTATED TNRC18 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              246
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNRC18 MUTATED     3   0   0   1
  TNRC18 WILD-TYPE 178  52   2   7
D20V5, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  R0              3              178
  R1              0               52
  R2              0                2
  RX              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, continuous
D20V7, continuous
D20V8, continuous
D20V9, continuous
D20V10, continuous
D20V11, continuous
D20V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNRC18 MUTATED       0                         0     2
  TNRC18 WILD-TYPE     2                         7   145
D20V13, multiclass
[1] "Remove cluster labels:" "TNRC18 MUTATED"        
clus
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7331       TCGA-EJ-7781 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7744 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 

Clustering(21) Variable = MED15 MUTATION ANALYSIS
D21V1, continuous
                 vv
clus               T2  T3  T4
  MED15 MUTATED     2   3   0
  MED15 WILD-TYPE 113 131   5
D21V2, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  T2             2             113
  T3             3             131
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V3, binary
                 cls
clus                0   1
  MED15 MUTATED     5   0
  MED15 WILD-TYPE 185  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      5    0
  MED15 WILD-TYPE  185   23
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0             5             185
  1             0              23
[1] 2 2
[1] FALSE
D21V4, binary
                 cls
clus                0   1
  MED15 MUTATED     0   5
  MED15 WILD-TYPE   6 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      0    5
  MED15 WILD-TYPE    6  245
                                        clus
vv                                       MED15 MUTATED MED15 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             245
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED15 MUTATED     4   1   0   0
  MED15 WILD-TYPE 177  51   2   8
D21V5, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  R0             4             177
  R1             1              51
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, continuous
D21V7, continuous
D21V8, continuous
D21V9, continuous
D21V10, continuous
D21V11, continuous
D21V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED15 MUTATED       0                         1     2
  MED15 WILD-TYPE     2                         6   145
D21V13, multiclass
                           clus
vv                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 2             145
[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"

Clustering(22) Variable = NKX3-1 MUTATION ANALYSIS
D22V1, continuous
                  vv
clus                T2  T3  T4
  NKX3-1 MUTATED     4   1   0
  NKX3-1 WILD-TYPE 111 133   5
D22V2, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  T2              4              111
  T3              1              133
  T4              0                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V3, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     5   0
  NKX3-1 WILD-TYPE 185  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      5    0
  NKX3-1 WILD-TYPE  185   23
   clus
vv  NKX3-1 MUTATED NKX3-1 WILD-TYPE
  0              5              185
  1              0               23
[1] 2 2
[1] FALSE
D22V4, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     0   5
  NKX3-1 WILD-TYPE   6 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      0    5
  NKX3-1 WILD-TYPE    6  245
                                        clus
vv                                       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              245
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NKX3-1 MUTATED     5   0   0   0
  NKX3-1 WILD-TYPE 176  52   2   8
D22V5, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  R0              5              176
  R1              0               52
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, continuous
D22V7, continuous
D22V8, continuous
D22V9, continuous
D22V10, continuous
D22V11, continuous
D22V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NKX3-1 MUTATED       0                         0     5
  NKX3-1 WILD-TYPE     2                         7   142
D22V13, multiclass
                           clus
vv                          NKX3-1 MUTATED NKX3-1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[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"

Clustering(23) Variable = KDM6A MUTATION ANALYSIS
D23V1, continuous
                 vv
clus               T2  T3  T4
  KDM6A MUTATED     6   0   0
  KDM6A WILD-TYPE 109 134   5
D23V2, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T2             6             109
  T3             0             134
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V3, binary
                 cls
clus                0   1
  KDM6A MUTATED     6   0
  KDM6A WILD-TYPE 184  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      6    0
  KDM6A WILD-TYPE  184   23
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             6             184
  1             0              23
[1] 2 2
[1] FALSE
D23V4, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   6
  KDM6A WILD-TYPE   6 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    6
  KDM6A WILD-TYPE    6  244
                                        clus
vv                                       KDM6A MUTATED KDM6A WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             244
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED     4   0   0   1
  KDM6A WILD-TYPE 177  52   2   7
D23V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0             4             177
  R1             0              52
  R2             0               2
  RX             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, continuous
D23V7, continuous
D23V8, continuous
D23V9, continuous
D23V10, continuous
D23V11, continuous
D23V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       0                         0     4
  KDM6A WILD-TYPE     2                         7   143
D23V13, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             143
[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"

Clustering(24) Variable = RNF31 MUTATION ANALYSIS
D24V1, continuous
                 vv
clus               T2  T3  T4
  RNF31 MUTATED     1   3   0
  RNF31 WILD-TYPE 114 131   5
D24V2, multiclass
    clus
vv   RNF31 MUTATED RNF31 WILD-TYPE
  T2             1             114
  T3             3             131
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V3, binary
                 cls
clus                0   1
  RNF31 MUTATED     4   0
  RNF31 WILD-TYPE 186  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF31 MUTATED      4    0
  RNF31 WILD-TYPE  186   23
   clus
vv  RNF31 MUTATED RNF31 WILD-TYPE
  0             4             186
  1             0              23
[1] 2 2
[1] FALSE
D24V4, binary
                 cls
clus                0   1
  RNF31 MUTATED     0   4
  RNF31 WILD-TYPE   6 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF31 MUTATED      0    4
  RNF31 WILD-TYPE    6  246
                                        clus
vv                                       RNF31 MUTATED RNF31 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             246
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF31 MUTATED     2   1   0   1
  RNF31 WILD-TYPE 179  51   2   7
D24V5, multiclass
    clus
vv   RNF31 MUTATED RNF31 WILD-TYPE
  R0             2             179
  R1             1              51
  R2             0               2
  RX             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, continuous
D24V7, continuous
D24V8, continuous
D24V9, continuous
D24V10, continuous
D24V11, continuous
D24V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF31 MUTATED       1                         0     1
  RNF31 WILD-TYPE     1                         7   146
D24V13, multiclass
[1] "Remove cluster labels:" "RNF31 MUTATED"         
clus
  RNF31 MUTATED RNF31 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"RNF31 WILD-TYPE" "RNF31 WILD-TYPE" 

Clustering(25) Variable = ESCO1 MUTATION ANALYSIS
D25V1, continuous
                 vv
clus               T2  T3  T4
  ESCO1 MUTATED     1   3   0
  ESCO1 WILD-TYPE 114 131   5
D25V2, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  T2             1             114
  T3             3             131
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V3, binary
                 cls
clus                0   1
  ESCO1 MUTATED     4   0
  ESCO1 WILD-TYPE 186  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      4    0
  ESCO1 WILD-TYPE  186   23
   clus
vv  ESCO1 MUTATED ESCO1 WILD-TYPE
  0             4             186
  1             0              23
[1] 2 2
[1] FALSE
D25V4, binary
                 cls
clus                0   1
  ESCO1 MUTATED     0   4
  ESCO1 WILD-TYPE   6 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      0    4
  ESCO1 WILD-TYPE    6  246
                                        clus
vv                                       ESCO1 MUTATED ESCO1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             246
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESCO1 MUTATED     2   1   0   0
  ESCO1 WILD-TYPE 179  51   2   8
D25V5, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  R0             2             179
  R1             1              51
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, continuous
D25V7, continuous
D25V8, continuous
D25V9, continuous
D25V10, continuous
D25V11, continuous
D25V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESCO1 MUTATED       0                         0     4
  ESCO1 WILD-TYPE     2                         7   143
D25V13, multiclass
                           clus
vv                          ESCO1 MUTATED ESCO1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             143
[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"

Clustering(26) Variable = LMOD2 MUTATION ANALYSIS
D26V1, continuous
                 vv
clus               T2  T3  T4
  LMOD2 MUTATED     2   1   0
  LMOD2 WILD-TYPE 113 133   5
D26V2, multiclass
    clus
vv   LMOD2 MUTATED LMOD2 WILD-TYPE
  T2             2             113
  T3             1             133
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V3, binary
                 cls
clus                0   1
  LMOD2 MUTATED     2   0
  LMOD2 WILD-TYPE 188  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      2    0
  LMOD2 WILD-TYPE  188   23
   clus
vv  LMOD2 MUTATED LMOD2 WILD-TYPE
  0             2             188
  1             0              23
[1] 2 2
[1] FALSE
D26V4, binary
                 cls
clus                0   1
  LMOD2 MUTATED     0   3
  LMOD2 WILD-TYPE   6 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      0    3
  LMOD2 WILD-TYPE    6  247
                                        clus
vv                                       LMOD2 MUTATED LMOD2 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             247
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMOD2 MUTATED     1   0   0   0
  LMOD2 WILD-TYPE 180  52   2   8
D26V5, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              1             242 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8472      TCGA-EJ-8474      TCGA-EJ-A46E      TCGA-EJ-A46F 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46G      TCGA-EJ-A46H      TCGA-EJ-A46I      TCGA-EJ-A65B 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65D      TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65J      TCGA-FC-7708      TCGA-FC-A4JI      TCGA-FC-A5OB 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A66V      TCGA-FC-A6HD      TCGA-G9-6329      TCGA-G9-6332 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6339 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6347      TCGA-G9-6348 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6354      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6385 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6498      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7523      TCGA-G9-7525      TCGA-H9-A6BX      TCGA-H9-A6BY 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7737      TCGA-HC-7738 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-8213 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-8216      TCGA-HC-8256      TCGA-HC-8257      TCGA-HC-8259 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-8260      TCGA-HC-8261      TCGA-HC-8262      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-8265      TCGA-HC-8266      TCGA-HC-A48F      TCGA-HC-A4ZV 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-A631      TCGA-HC-A632      TCGA-HC-A6AL      TCGA-HC-A6AN 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-A6AO      TCGA-HC-A6AP      TCGA-HC-A6AQ      TCGA-HC-A6AS 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-A6HX      TCGA-HC-A6HY      TCGA-HI-7168      TCGA-HI-7169 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171      TCGA-J4-8200      TCGA-J4-A67K 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-A67L      TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-A67R      TCGA-J4-A67S      TCGA-J4-A67T      TCGA-J4-A6G1 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-A6G3      TCGA-J4-A6M7      TCGA-J9-A52B      TCGA-J9-A52C 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J9-A52D      TCGA-J9-A52E      TCGA-KK-A59V      TCGA-KK-A59X 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Y      TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A6E0      TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A6E4      TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A6E8      TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-QU-A6IO      TCGA-QU-A6IP 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
D26V6, continuous
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              2             209 
     TCGA-CH-5737      TCGA-CH-5739      TCGA-CH-5740      TCGA-CH-5741 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745      TCGA-CH-5746 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7794      TCGA-EJ-7797 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8472 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8474      TCGA-EJ-A46D      TCGA-EJ-A46E      TCGA-EJ-A46F 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46G      TCGA-EJ-A65B      TCGA-EJ-A65D      TCGA-EJ-A65E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65F      TCGA-EJ-A65G      TCGA-EJ-A65J      TCGA-EJ-A65M 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A5OB      TCGA-FC-A66V 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A6HD      TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6338      TCGA-G9-6339      TCGA-G9-6348      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-G9-7510      TCGA-G9-7521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7522      TCGA-G9-7523      TCGA-G9-7525      TCGA-H9-A6BY 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7209 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213      TCGA-HC-7230 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7752      TCGA-HC-7818 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7821      TCGA-HC-8216      TCGA-HC-8257 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-8258      TCGA-HC-8260      TCGA-HC-8262      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-8265      TCGA-HC-8266      TCGA-HC-A48F      TCGA-HC-A4ZV 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-A631      TCGA-HC-A632      TCGA-HC-A6AL      TCGA-HC-A6AN 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-A6AS      TCGA-HC-A6HX      TCGA-HI-7168      TCGA-HI-7169 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171      TCGA-J4-8200      TCGA-J4-A67L 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O      TCGA-J4-A67R 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-A67S      TCGA-J4-A6G1      TCGA-J4-A6G3      TCGA-J9-A52B 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J9-A52E      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY      TCGA-KK-A6E0 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3      TCGA-KK-A6E4 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7      TCGA-KK-A6E8 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN      TCGA-QU-A6IO 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-QU-A6IP 
"LMOD2 WILD-TYPE" 
D26V7, continuous
D26V8, continuous
D26V9, continuous
D26V10, continuous
D26V11, continuous
D26V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LMOD2 MUTATED       0                         0     1
  LMOD2 WILD-TYPE     2                         7   146
D26V13, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213      TCGA-HC-7230 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 

Clustering(27) Variable = FAM120B MUTATION ANALYSIS
D27V1, continuous
                   vv
clus                 T2  T3  T4
  FAM120B MUTATED     1   2   0
  FAM120B WILD-TYPE 114 132   5
D27V2, multiclass
    clus
vv   FAM120B MUTATED FAM120B WILD-TYPE
  T2               1               114
  T3               2               132
  T4               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V3, binary
                   cls
clus                  0   1
  FAM120B MUTATED     2   0
  FAM120B WILD-TYPE 188  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      2    0
  FAM120B WILD-TYPE  188   23
   clus
vv  FAM120B MUTATED FAM120B WILD-TYPE
  0               2               188
  1               0                23
[1] 2 2
[1] FALSE
D27V4, binary
                   cls
clus                  0   1
  FAM120B MUTATED     0   3
  FAM120B WILD-TYPE   6 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      0    3
  FAM120B WILD-TYPE    6  247
                                        clus
vv                                       FAM120B MUTATED FAM120B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                 6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  3               247
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM120B MUTATED     3   0   0   0
  FAM120B WILD-TYPE 178  52   2   8
D27V5, multiclass
    clus
vv   FAM120B MUTATED FAM120B WILD-TYPE
  R0               3               178
  R1               0                52
  R2               0                 2
  RX               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, continuous
[1] "Remove cluster labels:" "FAM120B MUTATED"       
clus
  FAM120B MUTATED FAM120B WILD-TYPE 
                2               209 
       TCGA-CH-5737        TCGA-CH-5739        TCGA-CH-5740        TCGA-CH-5741 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745        TCGA-CH-5746 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7315 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8469 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-8470        TCGA-EJ-8472        TCGA-EJ-8474        TCGA-EJ-A46B 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A65B        TCGA-EJ-A65D        TCGA-EJ-A65E        TCGA-EJ-A65F 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A65G        TCGA-EJ-A65J        TCGA-EJ-A65M        TCGA-FC-7708 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-FC-7961        TCGA-FC-A5OB        TCGA-FC-A66V        TCGA-FC-A6HD 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6339        TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6361 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6377 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6379        TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-7523        TCGA-G9-7525        TCGA-H9-A6BY        TCGA-HC-7078 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7209        TCGA-HC-7210 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7740 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7752        TCGA-HC-7818 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7821        TCGA-HC-8216        TCGA-HC-8257 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-8258        TCGA-HC-8260        TCGA-HC-8262        TCGA-HC-8264 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HC-A48F        TCGA-HC-A4ZV 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-A631        TCGA-HC-A632        TCGA-HC-A6AL        TCGA-HC-A6AN 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-A6AS        TCGA-HC-A6HX        TCGA-HI-7168        TCGA-HI-7169 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8200        TCGA-J4-A67L 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-A67M        TCGA-J4-A67N        TCGA-J4-A67O        TCGA-J4-A67R 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-A67S        TCGA-J4-A6G1        TCGA-J4-A6G3        TCGA-J9-A52B 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1        TCGA-KK-A6DY        TCGA-KK-A6E0 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A6E1        TCGA-KK-A6E2        TCGA-KK-A6E3        TCGA-KK-A6E4 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A6E5        TCGA-KK-A6E6        TCGA-KK-A6E7        TCGA-KK-A6E8 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-QU-A6IL        TCGA-QU-A6IM        TCGA-QU-A6IN        TCGA-QU-A6IO 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-QU-A6IP 
"FAM120B WILD-TYPE" 
D27V7, continuous
D27V8, continuous
D27V9, continuous
D27V10, continuous
D27V11, continuous
D27V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM120B MUTATED       0                         0     3
  FAM120B WILD-TYPE     2                         7   144
D27V13, multiclass
                           clus
vv                          FAM120B MUTATED FAM120B WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               144
[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"

Clustering(28) Variable = CLEC1A MUTATION ANALYSIS
D28V1, continuous
                  vv
clus                T2  T3  T4
  CLEC1A MUTATED     1   2   1
  CLEC1A WILD-TYPE 114 132   4
D28V2, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  T2              1              114
  T3              2              132
  T4              1                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V3, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     3   0
  CLEC1A WILD-TYPE 187  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      3    0
  CLEC1A WILD-TYPE  187   23
   clus
vv  CLEC1A MUTATED CLEC1A WILD-TYPE
  0              3              187
  1              0               23
[1] 2 2
[1] FALSE
D28V4, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     0   4
  CLEC1A WILD-TYPE   6 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      0    4
  CLEC1A WILD-TYPE    6  246
                                        clus
vv                                       CLEC1A MUTATED CLEC1A WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              246
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLEC1A MUTATED     3   1   0   0
  CLEC1A WILD-TYPE 178  51   2   8
D28V5, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  R0              3              178
  R1              1               51
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, continuous
D28V7, continuous
D28V8, continuous
D28V9, continuous
D28V10, continuous
D28V11, continuous
D28V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLEC1A MUTATED       1                         0     1
  CLEC1A WILD-TYPE     1                         7   146
D28V13, multiclass
[1] "Remove cluster labels:" "CLEC1A MUTATED"        
clus
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125       TCGA-EJ-7314 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7327 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331       TCGA-EJ-7781 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736       TCGA-HC-7737 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742       TCGA-HC-7744 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"CLEC1A WILD-TYPE" "CLEC1A WILD-TYPE" 

Clustering(29) Variable = RNF17 MUTATION ANALYSIS
D29V1, continuous
                 vv
clus               T2  T3  T4
  RNF17 MUTATED     1   2   0
  RNF17 WILD-TYPE 114 132   5
D29V2, multiclass
    clus
vv   RNF17 MUTATED RNF17 WILD-TYPE
  T2             1             114
  T3             2             132
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V3, binary
                 cls
clus                0   1
  RNF17 MUTATED     3   0
  RNF17 WILD-TYPE 187  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF17 MUTATED      3    0
  RNF17 WILD-TYPE  187   23
   clus
vv  RNF17 MUTATED RNF17 WILD-TYPE
  0             3             187
  1             0              23
[1] 2 2
[1] FALSE
D29V4, binary
                 cls
clus                0   1
  RNF17 MUTATED     0   3
  RNF17 WILD-TYPE   6 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF17 MUTATED      0    3
  RNF17 WILD-TYPE    6  247
                                        clus
vv                                       RNF17 MUTATED RNF17 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             247
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF17 MUTATED     3   0   0   0
  RNF17 WILD-TYPE 178  52   2   8
D29V5, multiclass
    clus
vv   RNF17 MUTATED RNF17 WILD-TYPE
  R0             3             178
  R1             0              52
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, continuous
D29V7, continuous
D29V8, continuous
D29V9, continuous
D29V10, continuous
D29V11, continuous
[1] "Remove cluster labels:" "RNF17 MUTATED"         
clus
  RNF17 MUTATED RNF17 WILD-TYPE 
              2             252 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5741      TCGA-CH-5743 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5744      TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5517      TCGA-EJ-5518 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8472      TCGA-EJ-8474 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A46B      TCGA-EJ-A46D      TCGA-EJ-A46E      TCGA-EJ-A46F 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A46G      TCGA-EJ-A46H      TCGA-EJ-A46I      TCGA-EJ-A65B 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A65D      TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A65J      TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-FC-A4JI      TCGA-FC-A5OB      TCGA-FC-A66V      TCGA-FC-A6HD 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6338      TCGA-G9-6339      TCGA-G9-6342      TCGA-G9-6343 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6347      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6354      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6379      TCGA-G9-6384 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6498 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6499      TCGA-G9-7510      TCGA-G9-7519      TCGA-G9-7521 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-7522      TCGA-G9-7523      TCGA-G9-7525      TCGA-H9-7775 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-H9-A6BX      TCGA-H9-A6BY      TCGA-HC-7075      TCGA-HC-7077 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231      TCGA-HC-7232 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7750 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7752      TCGA-HC-7817      TCGA-HC-7818      TCGA-HC-7819 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HC-8213      TCGA-HC-8216 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8256      TCGA-HC-8257      TCGA-HC-8258      TCGA-HC-8259 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8260      TCGA-HC-8261      TCGA-HC-8262      TCGA-HC-8264 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8265      TCGA-HC-8266      TCGA-HC-A48F      TCGA-HC-A4ZV 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A631      TCGA-HC-A632      TCGA-HC-A6AL      TCGA-HC-A6AN 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A6AO      TCGA-HC-A6AP      TCGA-HC-A6AQ      TCGA-HC-A6AS 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A6HX      TCGA-HC-A6HY      TCGA-HI-7168      TCGA-HI-7169 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171      TCGA-J4-8198      TCGA-J4-8200 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A67K      TCGA-J4-A67L      TCGA-J4-A67M      TCGA-J4-A67N 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A67O      TCGA-J4-A67Q      TCGA-J4-A67R      TCGA-J4-A67S 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A67T      TCGA-J4-A6G1      TCGA-J4-A6G3      TCGA-J4-A6M7 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J9-A52B      TCGA-J9-A52C      TCGA-J9-A52D      TCGA-J9-A52E 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y      TCGA-KK-A59Z 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A5A1      TCGA-KK-A6DY      TCGA-KK-A6E0      TCGA-KK-A6E1 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A6E2      TCGA-KK-A6E3      TCGA-KK-A6E4      TCGA-KK-A6E5 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A6E6      TCGA-KK-A6E7      TCGA-KK-A6E8      TCGA-QU-A6IL 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-QU-A6IM      TCGA-QU-A6IN      TCGA-QU-A6IO      TCGA-QU-A6IP 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
D29V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF17 MUTATED       0                         0     3
  RNF17 WILD-TYPE     2                         7   144
D29V13, multiclass
                           clus
vv                          RNF17 MUTATED RNF17 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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"

Clustering(30) Variable = RP1L1 MUTATION ANALYSIS
D30V1, continuous
                 vv
clus               T2  T3  T4
  RP1L1 MUTATED     3   4   0
  RP1L1 WILD-TYPE 112 130   5
D30V2, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  T2             3             112
  T3             4             130
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V3, binary
                 cls
clus                0   1
  RP1L1 MUTATED     5   0
  RP1L1 WILD-TYPE 185  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      5    0
  RP1L1 WILD-TYPE  185   23
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0             5             185
  1             0              23
[1] 2 2
[1] FALSE
D30V4, binary
                 cls
clus                0   1
  RP1L1 MUTATED     0   7
  RP1L1 WILD-TYPE   6 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      0    7
  RP1L1 WILD-TYPE    6  243
                                        clus
vv                                       RP1L1 MUTATED RP1L1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             243
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RP1L1 MUTATED     4   1   0   1
  RP1L1 WILD-TYPE 177  51   2   7
D30V5, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  R0             4             177
  R1             1              51
  R2             0               2
  RX             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, continuous
D30V7, continuous
D30V8, continuous
D30V9, continuous
D30V10, continuous
D30V11, continuous
D30V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RP1L1 MUTATED       0                         0     2
  RP1L1 WILD-TYPE     2                         7   145
D30V13, multiclass
[1] "Remove cluster labels:" "RP1L1 MUTATED"         
clus
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5526      TCGA-EJ-5527 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 

Clustering(31) Variable = EOMES MUTATION ANALYSIS
D31V1, continuous
                 vv
clus               T2  T3  T4
  EOMES MUTATED     1   2   1
  EOMES WILD-TYPE 114 132   4
D31V2, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  T2             1             114
  T3             2             132
  T4             1               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V3, binary
                 cls
clus                0   1
  EOMES MUTATED     3   0
  EOMES WILD-TYPE 187  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      3    0
  EOMES WILD-TYPE  187   23
   clus
vv  EOMES MUTATED EOMES WILD-TYPE
  0             3             187
  1             0              23
[1] 2 2
[1] FALSE
D31V4, binary
                 cls
clus                0   1
  EOMES MUTATED     0   4
  EOMES WILD-TYPE   6 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    4
  EOMES WILD-TYPE    6  246
                                        clus
vv                                       EOMES MUTATED EOMES WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             246
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EOMES MUTATED     1   3   0   0
  EOMES WILD-TYPE 180  49   2   8
D31V5, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             1             180
  R1             3              49
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, continuous
D31V7, continuous
D31V8, continuous
D31V9, continuous
D31V10, continuous
D31V11, continuous
D31V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EOMES MUTATED       0                         0     1
  EOMES WILD-TYPE     2                         7   146
D31V13, multiclass
[1] "Remove cluster labels:" "EOMES MUTATED"         
clus
  EOMES MUTATED EOMES WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6366      TCGA-G9-6367 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 

Clustering(32) Variable = MTF1 MUTATION ANALYSIS
D32V1, continuous
                vv
clus              T2  T3  T4
  MTF1 MUTATED     1   2   0
  MTF1 WILD-TYPE 114 132   5
D32V2, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  T2            1            114
  T3            2            132
  T4            0              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V3, binary
                cls
clus               0   1
  MTF1 MUTATED     2   0
  MTF1 WILD-TYPE 188  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      2    0
  MTF1 WILD-TYPE  188   23
   clus
vv  MTF1 MUTATED MTF1 WILD-TYPE
  0            2            188
  1            0             23
[1] 2 2
[1] FALSE
D32V4, binary
                cls
clus               0   1
  MTF1 MUTATED     0   3
  MTF1 WILD-TYPE   6 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      0    3
  MTF1 WILD-TYPE    6  247
                                        clus
vv                                       MTF1 MUTATED MTF1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0              6
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            247
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTF1 MUTATED     2   1   0   0
  MTF1 WILD-TYPE 179  51   2   8
D32V5, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  R0            2            179
  R1            1             51
  R2            0              2
  RX            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, continuous
[1] "Remove cluster labels:" "MTF1 MUTATED"          
clus
  MTF1 MUTATED MTF1 WILD-TYPE 
             2            209 
    TCGA-CH-5737     TCGA-CH-5739     TCGA-CH-5740     TCGA-CH-5741 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745     TCGA-CH-5746 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7794     TCGA-EJ-7797 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-8468     TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8472 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-8474     TCGA-EJ-A46B     TCGA-EJ-A46D     TCGA-EJ-A46E 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A46F     TCGA-EJ-A46G     TCGA-EJ-A65B     TCGA-EJ-A65D 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-EJ-A65E     TCGA-EJ-A65F     TCGA-EJ-A65J     TCGA-EJ-A65M 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-FC-A5OB     TCGA-FC-A66V 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-FC-A6HD     TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6338     TCGA-G9-6339     TCGA-G9-6348     TCGA-G9-6356 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6379     TCGA-G9-6384     TCGA-G9-6494 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-G9-7522     TCGA-G9-7525     TCGA-H9-A6BY     TCGA-HC-7078 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7752     TCGA-HC-7818 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-8258     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8264 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-8265     TCGA-HC-8266     TCGA-HC-A48F     TCGA-HC-A4ZV 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-A631     TCGA-HC-A632     TCGA-HC-A6AL     TCGA-HC-A6AN 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HC-A6AS     TCGA-HC-A6HX     TCGA-HI-7168     TCGA-HI-7169 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171     TCGA-J4-8200     TCGA-J4-A67L 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-J4-A67M     TCGA-J4-A67N     TCGA-J4-A67O     TCGA-J4-A67R 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-J4-A67S     TCGA-J4-A6G1     TCGA-J4-A6G3     TCGA-J9-A52B 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-J9-A52E     TCGA-KK-A59V     TCGA-KK-A59X     TCGA-KK-A59Y 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KK-A59Z     TCGA-KK-A5A1     TCGA-KK-A6DY     TCGA-KK-A6E0 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KK-A6E1     TCGA-KK-A6E2     TCGA-KK-A6E3     TCGA-KK-A6E4 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-KK-A6E5     TCGA-KK-A6E6     TCGA-KK-A6E7     TCGA-KK-A6E8 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-QU-A6IL     TCGA-QU-A6IM     TCGA-QU-A6IN     TCGA-QU-A6IO 
"MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" "MTF1 WILD-TYPE" 
    TCGA-QU-A6IP 
"MTF1 WILD-TYPE" 
D32V7, continuous
D32V8, continuous
D32V9, continuous
D32V10, continuous
D32V11, continuous
D32V12, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTF1 MUTATED       0                         0     0
  MTF1 WILD-TYPE     2                         7   147
D32V13, multiclass

Clustering(33) Variable = NTM MUTATION ANALYSIS
D33V1, continuous
               vv
clus             T2  T3  T4
  NTM MUTATED     1   4   0
  NTM WILD-TYPE 114 130   5
D33V2, multiclass
    clus
vv   NTM MUTATED NTM WILD-TYPE
  T2           1           114
  T3           4           130
  T4           0             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V3, binary
               cls
clus              0   1
  NTM MUTATED     5   0
  NTM WILD-TYPE 185  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  NTM MUTATED      5    0
  NTM WILD-TYPE  185   23
   clus
vv  NTM MUTATED NTM WILD-TYPE
  0           5           185
  1           0            23
[1] 2 2
[1] FALSE
D33V4, binary
               cls
clus              0   1
  NTM MUTATED     0   5
  NTM WILD-TYPE   6 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  NTM MUTATED      0    5
  NTM WILD-TYPE    6  245
                                        clus
vv                                       NTM MUTATED NTM WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE           0             6
  PROSTATE ADENOCARCINOMA ACINAR TYPE              5           245
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NTM MUTATED     3   2   0   0
  NTM WILD-TYPE 178  50   2   8
D33V5, multiclass
    clus
vv   NTM MUTATED NTM WILD-TYPE
  R0           3           178
  R1           2            50
  R2           0             2
  RX           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, continuous
D33V7, continuous
D33V8, continuous
D33V9, continuous
D33V10, continuous
D33V11, continuous
D33V12, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NTM MUTATED       0                         0     5
  NTM WILD-TYPE     2                         7   142
D33V13, multiclass
                           clus
vv                          NTM MUTATED NTM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             7
  WHITE                               5           142
[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"

Clustering(34) Variable = FNBP4 MUTATION ANALYSIS
D34V1, continuous
                 vv
clus               T2  T3  T4
  FNBP4 MUTATED     0   3   0
  FNBP4 WILD-TYPE 115 131   5
D34V2, multiclass
    clus
vv   FNBP4 MUTATED FNBP4 WILD-TYPE
  T2             0             115
  T3             3             131
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V3, binary
                 cls
clus                0   1
  FNBP4 MUTATED     2   1
  FNBP4 WILD-TYPE 188  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNBP4 MUTATED      2    1
  FNBP4 WILD-TYPE  188   22
   clus
vv  FNBP4 MUTATED FNBP4 WILD-TYPE
  0             2             188
  1             1              22
[1] 2 2
[1] FALSE
D34V4, binary
                 cls
clus                0   1
  FNBP4 MUTATED     0   3
  FNBP4 WILD-TYPE   6 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNBP4 MUTATED      0    3
  FNBP4 WILD-TYPE    6  247
                                        clus
vv                                       FNBP4 MUTATED FNBP4 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             247
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FNBP4 MUTATED     1   2   0   0
  FNBP4 WILD-TYPE 180  50   2   8
D34V5, multiclass
    clus
vv   FNBP4 MUTATED FNBP4 WILD-TYPE
  R0             1             180
  R1             2              50
  R2             0               2
  RX             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, continuous
D34V7, continuous
D34V8, continuous
D34V9, continuous
D34V10, continuous
D34V11, continuous
D34V12, continuous
[1] "Remove cluster labels:" "FNBP4 MUTATED"         
clus
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              2             217 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5495 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8472 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D      TCGA-EJ-A46E 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A46H      TCGA-EJ-A46I 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A65B      TCGA-EJ-A65D      TCGA-EJ-A65E      TCGA-EJ-A65F 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-A65G      TCGA-EJ-A65J      TCGA-EJ-A65M      TCGA-FC-A5OB 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-FC-A66V      TCGA-FC-A6HD      TCGA-G9-6329      TCGA-G9-6332 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6339 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6347      TCGA-G9-6348 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6354      TCGA-G9-6356 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6377      TCGA-G9-6378 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6498      TCGA-G9-6499      TCGA-G9-7510 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7525 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-H9-7775      TCGA-H9-A6BX      TCGA-HC-7075      TCGA-HC-7077 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7209 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7230      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7817      TCGA-HC-7818 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7821      TCGA-HC-8216      TCGA-HC-8258 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-8259      TCGA-HC-8260      TCGA-HC-8262      TCGA-HC-8265 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J4-A67K      TCGA-J4-A67L 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O      TCGA-J4-A67Q 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-A67R      TCGA-J4-A67S      TCGA-J4-A67T      TCGA-J4-A6G1 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J4-A6G3      TCGA-J4-A6M7      TCGA-J9-A52B      TCGA-J9-A52C 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-J9-A52D      TCGA-J9-A52E      TCGA-KK-A59V      TCGA-KK-A59Y 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY      TCGA-KK-A6E0 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3      TCGA-KK-A6E4 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7      TCGA-KK-A6E8 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN      TCGA-QU-A6IO 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-QU-A6IP 
"FNBP4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FNBP4 MUTATED       0                         1     0
  FNBP4 WILD-TYPE     2                         6   147
D34V13, multiclass
[1] "Remove cluster labels:" "FNBP4 MUTATED"         
clus
  FNBP4 MUTATED FNBP4 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7791 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" "FNBP4 WILD-TYPE" 

Clustering(35) Variable = CDKN1B MUTATION ANALYSIS
D35V1, continuous
                  vv
clus                T2  T3  T4
  CDKN1B MUTATED     1   2   1
  CDKN1B WILD-TYPE 114 132   4
D35V2, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  T2              1              114
  T3              2              132
  T4              1                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V3, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     4   0
  CDKN1B WILD-TYPE 186  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      4    0
  CDKN1B WILD-TYPE  186   23
   clus
vv  CDKN1B MUTATED CDKN1B WILD-TYPE
  0              4              186
  1              0               23
[1] 2 2
[1] FALSE
D35V4, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     0   4
  CDKN1B WILD-TYPE   6 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      0    4
  CDKN1B WILD-TYPE    6  246
                                        clus
vv                                       CDKN1B MUTATED CDKN1B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0                6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              246
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDKN1B MUTATED     3   1   0   0
  CDKN1B WILD-TYPE 178  51   2   8
D35V5, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  R0              3              178
  R1              1               51
  R2              0                2
  RX              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, continuous
D35V7, continuous
D35V8, continuous
D35V9, continuous
D35V10, continuous
D35V11, continuous
D35V12, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN1B MUTATED       0                         0     3
  CDKN1B WILD-TYPE     2                         7   144
D35V13, multiclass
                           clus
vv                          CDKN1B MUTATED CDKN1B WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[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"

Clustering(36) Variable = EIF2AK3 MUTATION ANALYSIS
D36V1, continuous
                   vv
clus                 T2  T3  T4
  EIF2AK3 MUTATED     2   2   0
  EIF2AK3 WILD-TYPE 113 132   5
D36V2, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  T2               2               113
  T3               2               132
  T4               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V3, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     2   0
  EIF2AK3 WILD-TYPE 188  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      2    0
  EIF2AK3 WILD-TYPE  188   23
   clus
vv  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  0               2               188
  1               0                23
[1] 2 2
[1] FALSE
D36V4, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     0   4
  EIF2AK3 WILD-TYPE   6 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      0    4
  EIF2AK3 WILD-TYPE    6  246
                                        clus
vv                                       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                 6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               246
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EIF2AK3 MUTATED     2   1   0   1
  EIF2AK3 WILD-TYPE 179  51   2   7
D36V5, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  R0               2               179
  R1               1                51
  R2               0                 2
  RX               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, continuous
[1] "Remove cluster labels:" "EIF2AK3 MUTATED"       
clus
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                2               209 
       TCGA-CH-5737        TCGA-CH-5739        TCGA-CH-5740        TCGA-CH-5741 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745        TCGA-CH-5746 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5763 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-8470        TCGA-EJ-8472        TCGA-EJ-8474        TCGA-EJ-A46B 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-A65B        TCGA-EJ-A65D        TCGA-EJ-A65E        TCGA-EJ-A65F 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-EJ-A65G        TCGA-EJ-A65J        TCGA-EJ-A65M        TCGA-FC-7708 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-FC-7961        TCGA-FC-A5OB        TCGA-FC-A66V        TCGA-FC-A6HD 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6339        TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6361 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6377 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6379        TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-G9-7523        TCGA-G9-7525        TCGA-H9-A6BY        TCGA-HC-7078 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7209        TCGA-HC-7210 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7740 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7752        TCGA-HC-7818 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7821        TCGA-HC-8216        TCGA-HC-8257 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-8258        TCGA-HC-8260        TCGA-HC-8262        TCGA-HC-8264 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HC-A48F        TCGA-HC-A4ZV 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-A631        TCGA-HC-A632        TCGA-HC-A6AL        TCGA-HC-A6AN 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HC-A6AS        TCGA-HC-A6HX        TCGA-HI-7168        TCGA-HI-7169 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8200        TCGA-J4-A67L 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-J4-A67M        TCGA-J4-A67N        TCGA-J4-A67O        TCGA-J4-A67R 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-J4-A67S        TCGA-J4-A6G1        TCGA-J4-A6G3        TCGA-J9-A52B 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1        TCGA-KK-A6DY        TCGA-KK-A6E0 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KK-A6E1        TCGA-KK-A6E2        TCGA-KK-A6E3        TCGA-KK-A6E4 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-KK-A6E5        TCGA-KK-A6E6        TCGA-KK-A6E7        TCGA-KK-A6E8 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-QU-A6IL        TCGA-QU-A6IM        TCGA-QU-A6IN        TCGA-QU-A6IO 
"EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" "EIF2AK3 WILD-TYPE" 
       TCGA-QU-A6IP 
"EIF2AK3 WILD-TYPE" 
D36V7, continuous
D36V8, continuous
D36V9, continuous
D36V10, continuous
D36V11, continuous
D36V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF2AK3 MUTATED       0                         0     3
  EIF2AK3 WILD-TYPE     2                         7   144
D36V13, multiclass
                           clus
vv                          EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               144
[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"

Clustering(37) Variable = LARP1 MUTATION ANALYSIS
D37V1, continuous
                 vv
clus               T2  T3  T4
  LARP1 MUTATED     1   2   0
  LARP1 WILD-TYPE 114 132   5
D37V2, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  T2             1             114
  T3             2             132
  T4             0               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V3, binary
                 cls
clus                0   1
  LARP1 MUTATED     2   1
  LARP1 WILD-TYPE 188  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      2    1
  LARP1 WILD-TYPE  188   22
   clus
vv  LARP1 MUTATED LARP1 WILD-TYPE
  0             2             188
  1             1              22
[1] 2 2
[1] FALSE
D37V4, binary
                 cls
clus                0   1
  LARP1 MUTATED     0   3
  LARP1 WILD-TYPE   6 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      0    3
  LARP1 WILD-TYPE    6  247
                                        clus
vv                                       LARP1 MUTATED LARP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0               6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             247
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP1 MUTATED     2   0   0   0
  LARP1 WILD-TYPE 179  52   2   8
D37V5, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             241 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5521 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8472      TCGA-EJ-8474 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-A46B      TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-A46H      TCGA-EJ-A46I      TCGA-EJ-A65B      TCGA-EJ-A65D 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G      TCGA-EJ-A65J 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-A4JI      TCGA-FC-A5OB      TCGA-FC-A66V 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-A6HD      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6339      TCGA-G9-6342 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6347      TCGA-G9-6348      TCGA-G9-6351 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6354      TCGA-G9-6356      TCGA-G9-6361 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6498      TCGA-G9-6499      TCGA-G9-7510 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-A6BX      TCGA-H9-A6BY      TCGA-HC-7075 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231      TCGA-HC-7232 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7233      TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7748 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-8213      TCGA-HC-8216 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-8256      TCGA-HC-8257      TCGA-HC-8259      TCGA-HC-8260 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-8261      TCGA-HC-8262      TCGA-HC-8264      TCGA-HC-8265 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-8266      TCGA-HC-A48F      TCGA-HC-A4ZV      TCGA-HC-A631 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-A632      TCGA-HC-A6AL      TCGA-HC-A6AN      TCGA-HC-A6AO 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-A6AP      TCGA-HC-A6AQ      TCGA-HC-A6AS      TCGA-HC-A6HX 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-A6HY      TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HI-7171      TCGA-J4-8200      TCGA-J4-A67K      TCGA-J4-A67L 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O      TCGA-J4-A67R 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J4-A67S      TCGA-J4-A67T      TCGA-J4-A6G1      TCGA-J4-A6G3 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J4-A6M7      TCGA-J9-A52B      TCGA-J9-A52C      TCGA-J9-A52D 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-J9-A52E      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY      TCGA-KK-A6E0 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3      TCGA-KK-A6E4 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7      TCGA-KK-A6E8 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN      TCGA-QU-A6IO 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-QU-A6IP 
"LARP1 WILD-TYPE" 
D37V6, continuous
D37V7, continuous
D37V8, continuous
D37V9, continuous
D37V10, continuous
D37V11, continuous
D37V12, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP1 MUTATED       0                         0     2
  LARP1 WILD-TYPE     2                         7   145
D37V13, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5521      TCGA-EJ-5522 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5530 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
