[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"        "-oTHNSC-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/HNSC-TP/11541491/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/10686792/transformed.cor.cli.txt"

nPatients in clinical file=494, in cluster file=306, common to both=306
[1]  27 306
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           213             93 
  TP53 MUTATED TP53 WILD-TYPE 
           213             93 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              65              241 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              65              241 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             27             279 
  CASP8 MUTATED CASP8 WILD-TYPE 
             27             279 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            69            237 
  FAT1 MUTATED FAT1 WILD-TYPE 
            69            237 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            53            253 
  MLL2 MUTATED MLL2 WILD-TYPE 
            53            253 
[1] "JUB MUTATION ANALYSIS"
[1] 3
  JUB MUTATED JUB WILD-TYPE 
           18           288 
  JUB MUTATED JUB WILD-TYPE 
           18           288 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              57              249 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              57              249 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              17              289 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              17              289 
[1] "NSD1 MUTATION ANALYSIS"
[1] 3
  NSD1 MUTATED NSD1 WILD-TYPE 
            33            273 
  NSD1 MUTATED NSD1 WILD-TYPE 
            33            273 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            10            296 
  HRAS MUTATED HRAS WILD-TYPE 
            10            296 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              13              293 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              13              293 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             14             292 
  RASA1 MUTATED RASA1 WILD-TYPE 
             14             292 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
              9             297 
  HLA-A MUTATED HLA-A WILD-TYPE 
              9             297 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             13             293 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             13             293 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
             9            297 
  RAC1 MUTATED RAC1 WILD-TYPE 
             9            297 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             24             282 
  EP300 MUTATED EP300 WILD-TYPE 
             24             282 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              10              296 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              10              296 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              64              242 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              64              242 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             15             291 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             15             291 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           10           296 
  RB1 MUTATED RB1 WILD-TYPE 
           10           296 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            11            295 
  CTCF MUTATED CTCF WILD-TYPE 
            11            295 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              8             298 
  KDM6A MUTATED KDM6A WILD-TYPE 
              8             298 
[1] "ELF4 MUTATION ANALYSIS"
[1] 3
  ELF4 MUTATED ELF4 WILD-TYPE 
             5            301 
  ELF4 MUTATED ELF4 WILD-TYPE 
             5            301 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
             4            302 
  RHOA MUTATED RHOA WILD-TYPE 
             4            302 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              8             298 
  HLA-B MUTATED HLA-B WILD-TYPE 
              8             298 
[1] "PRSS1 MUTATION ANALYSIS"
[1] 3
  PRSS1 MUTATED PRSS1 WILD-TYPE 
              7             299 
  PRSS1 MUTATED PRSS1 WILD-TYPE 
              7             299 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               8              298 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               8              298 
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 306 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415           NA          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
          NA         1330          811         1268           NA         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
        1045          173           NA         1081         1681           NA 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
          NA           NA           NA           NA           NA           NA 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98           NA 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202         1110          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
         735           NA          432          429           46         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1207          654           NA         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
        1399          317          129         1253           NA           NA 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
        1000         1407         1057          985           NA           NA 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 
          NA         1179         1007          509         1309         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
          NA         1050         1125           NA          514           NA 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479           NA         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245           NA          105           NA          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
          30          972           NA         1036           NA          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
          NA          997         1430           NA          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         4241 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         3930         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        3270         2886         2327         2784         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        1315         1665          641         1899           NA           NA 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
          NA           NA         3835           NA           NA           NA 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         3381           NA           NA           NA           NA 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
          NA         3497         2347           NA         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
         954          797           NA           NA           NA           NA 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
          NA           NA           NA         1099           NA           NA 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
          NA           NA         4335           NA           NA           NA 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
         317          321          237          828           NA          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548           NA 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          299          368          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
        1131          407            2            5           25           NA 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          NA           37         1057          485          122          441 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=131,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=197,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "GENDER"                                
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [7] "NUMBERPACKYEARSSMOKED"                 
 [8] "NUMBER.OF.LYMPH.NODES"                 
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 306 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=56, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 24  77  63 101 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 24  77  63 101 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 24  77  63 101 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 24  77  63 101 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
99 33 99  5 
[1] "table(vv)"
vv
N0 N1 N2 N3 
99 33 99  5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
99 33 99  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
99 33 99  5 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=70, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=25, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   103  73
  TP53 WILD-TYPE  65  18
  TP53 MUTATED TP53 WILD-TYPE 
           176             83 
  TP53 MUTATED TP53 WILD-TYPE 
            73             18 
$`TP53 MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          283          415          276          722         1288 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         520          623         1636          190          644          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
         384          113          236          187          278          133 
TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         536         1153          428          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1230         1151          392          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         395          625         1960         1330          811         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 
        1966         1966         1975          683          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5329 
         394          735          432          429           46         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1407         1057          985         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 
        1007          509         1971          514         1969          354 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 
         350         1956         1435         1191         1245          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          759           30          972         1968         1036 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7393 TCGA-CR-7394 
        1954         1430         1951          907          908          898 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
         216          156          181          911         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
         215         1315         1665         1899         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         3837         1959         1970         1970         1936 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1987         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7422 
         954          797         1967         1976         1955         1957 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1947         1972         1937         1984         1958         1959 
TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         317          237          828          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         491          154         1778          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-HD-7229 TCGA-HD-7753 
        1965          299          324         1131            2            5 
TCGA-HD-7917 TCGA-IQ-7630 
          37          485 

$`TP53 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6871 
        1983          248         1762          725         1747           63 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        2878          140          558          310          423          687 
TCGA-BB-7866 TCGA-BB-7872 TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4741 TCGA-CN-5355 
         638          436          817          758         1268         1007 
TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        1681          290          630         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-6227 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1660         1959         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1125          362          311          345          234          379 
TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7385 
         479         1440         1960          889          796          997 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7404 
         392          913          946          930         1077         1472 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6441 
        2886         2327         1958          701          641         1970 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7250 TCGA-CV-7261 
        1957         1959         1959         1979         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7440 TCGA-CX-7085 TCGA-D6-6516 
        1974         1948         1937         1981          321          773 
TCGA-D6-6827 TCGA-DQ-5625 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
         568         1081          575          775          622          368 
TCGA-H7-7774 TCGA-HD-7754 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
         407           25         1057          122          441 

  TP53 MUTATED TP53 WILD-TYPE 
             2             25 
  TP53 MUTATED TP53 WILD-TYPE 
          3837           2886 
  TP53 MUTATED TP53 WILD-TYPE 
        1003.5          946.0 
[1] "2.0 - 3837.0 (1003.5)" "25.0 - 2886.0 (946.0)"
[1] "hr=" "1.8"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TP53 MUTATED         8       28        31       117         6
  TP53 WILD-TYPE       9       18        11        32         0
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              8              9
  STAGE II            28             18
  STAGE III           31             11
  STAGE IVA          117             32
  STAGE IVB            6              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED   13 49 53 78
  TP53 WILD-TYPE 11 28 10 23
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           13             11
  T2           49             28
  T3           53             10
  T4           78             23
[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"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   64 24 82  5
  TP53 WILD-TYPE 35  9 17  0
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           64             35
  N1           24              9
  N2           82             17
  N3            5              0
[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, binary
                cls
clus               0   1
  TP53 MUTATED    60 153
  TP53 WILD-TYPE  24  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     60  153
  TP53 WILD-TYPE   24   69
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           60             24
  MALE            153             69
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    62 151
  TP53 WILD-TYPE  19  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     62  151
  TP53 WILD-TYPE   19   74
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            62             19
  YES          151             74
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1     3
  TP53 WILD-TYPE                                0     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          22   180
  TP53 WILD-TYPE                         6    85
D1V10, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3              2
  BLACK OR AFRICAN AMERICAN                  22              6
  WHITE                                     180             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                cls
clus               0   1
  TP53 MUTATED    12 196
  TP53 WILD-TYPE   2  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     12  196
  TP53 WILD-TYPE    2   87
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO               12              2
  NOT HISPANIC OR LATINO          196             87
[1] 2 2
[1] FALSE

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    33  19
  CDKN2A WILD-TYPE 135  72
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              52              207 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              19               72 
$`CDKN2A MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-6873 
         283          276          623         1636          384          113 
TCGA-BA-7269 TCGA-BB-7862 TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-5359 
         236          536          721          395         1960         1980 
TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6021 
        1081         1975          683          629          628         1970 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-6224 
         432          429           46         1393         1399          985 
TCGA-CQ-6229 TCGA-CR-5247 TCGA-CR-6492 TCGA-CR-7370 TCGA-CR-7386 TCGA-CR-7394 
        1179          358          479          105         1430          898 
TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        1950         1978         2437         2641         1478         1840 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1665         1899         1959         3835         1948         1969 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7424 
        1939         1987          954          797         1976         1947 
TCGA-CV-7432 TCGA-D6-6516 TCGA-D6-6825 TCGA-DQ-5629 
        1937          773          491          516 

$`CDKN2A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        1762          520          725         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         451           63          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        1153          428          436         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
        1151          392          817          993          642          758 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
        1250          625         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
        1007         1045          173         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 
        1966         1966          290          630          933          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
         629           45          432           98          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CQ-5323 
         224          318          611          394          735         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-5334 
        1207          654         1660         1422          317          129 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6227 
        1253         1974         1000         1407         1057         1959 
TCGA-CQ-6228 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5248 
        1959         1007          509         1309         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 
         345          354          234          379          350         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        1435         1191         1440         1245         1960         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         913          946          908          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        3295         1438          584          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 
        1958          519          406          701          215         1315 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6952 
         641         1970         1948         1969         1952         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1970         1936         1959         1945         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
        1444         1095         1967         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1948         1955         1957         1937         1972         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1958         1959         1981          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
         828          292          701           77          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778         1081         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
         407            2            5           25           37         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         485          122          441 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
              46                2 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            3835             3837 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1130              993 
[1] "46.0 - 3835.0 (1130.0)" "2.0 - 3837.0 (993.0)"  
[1] "hr=" "1.2"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CDKN2A MUTATED         3        8        14        29         2
  CDKN2A WILD-TYPE      14       38        28       120         4
D2V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                3               14
  STAGE II               8               38
  STAGE III             14               28
  STAGE IVA             29              120
  STAGE IVB              2                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CDKN2A MUTATED    5 14 17 22
  CDKN2A WILD-TYPE 19 63 46 79
D2V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              5               19
  T2             14               63
  T3             17               46
  T4             22               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDKN2A MUTATED   21  8 20  1
  CDKN2A WILD-TYPE 78 25 79  4
D2V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             21               78
  N1              8               25
  N2             20               79
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    16  49
  CDKN2A WILD-TYPE  68 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     16   49
  CDKN2A WILD-TYPE   68  173
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             16               68
  MALE               49              173
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    20  45
  CDKN2A WILD-TYPE  61 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     20   45
  CDKN2A WILD-TYPE   61  180
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              20               61
  YES             45              180
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     1
  CDKN2A WILD-TYPE                                1     4
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           4    57
  CDKN2A WILD-TYPE                        24   208
D2V10, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                4
  BLACK OR AFRICAN AMERICAN                     4               24
  WHITE                                        57              208
[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"
D2V11, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     5  60
  CDKN2A WILD-TYPE   9 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5   60
  CDKN2A WILD-TYPE    9  223
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  5                9
  NOT HISPANIC OR LATINO             60              223
[1] 2 2
[1] FALSE

Clustering(3) Variable = CASP8 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    15   5
  CASP8 WILD-TYPE 153  86
  CASP8 MUTATED CASP8 WILD-TYPE 
             20             239 
  CASP8 MUTATED CASP8 WILD-TYPE 
              5              86 
$`CASP8 MUTATED`
TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6873 TCGA-CN-4734 TCGA-CQ-5324 TCGA-CQ-5327 
         722          725          113          758         1207         1660 
TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7068 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7394 
        1399          129         1309         1036          796          898 
TCGA-CR-7395 TCGA-CR-7402 TCGA-CV-5966 TCGA-CV-6436 TCGA-CV-6943 TCGA-CV-7095 
         930          911          519         1899         1948         1970 
TCGA-CV-7099 TCGA-CX-7085 
        1936          321 

$`CASP8 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          520          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
         190          644          451           63          384          236 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         428          436          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1681         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202         1110          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5325 
         735          432          429           46         1466          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1422         1393          317         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
        1007          509         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         913          946          908          216          156          181 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 
        1840          215         1315         1665          641         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        1948         1969         1952         1959         3835         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        1958         1959         1981          317          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         568         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1965          575          775          622          299          368 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         324         1131          407            2            5           25 
TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          37         1057          485          122          441 

  CASP8 MUTATED CASP8 WILD-TYPE 
            113               2 
  CASP8 MUTATED CASP8 WILD-TYPE 
           1970            3837 
  CASP8 MUTATED CASP8 WILD-TYPE 
          920.5          1000.0 
[1] "113.0 - 1970.0 (920.5)" "2.0 - 3837.0 (1000.0)" 
[1] "hr=" "1.4"
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CASP8 MUTATED         1        8         5        11         0
  CASP8 WILD-TYPE      16       38        37       138         6
D3V3, multiclass
           clus
vv          CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I               1              16
  STAGE II              8              38
  STAGE III             5              37
  STAGE IVA            11             138
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  CASP8 MUTATED    1 10  7  8
  CASP8 WILD-TYPE 23 67 56 93
D3V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             1              23
  T2            10              67
  T3             7              56
  T4             8              93
[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"
                 vv
clus              N0 N1 N2 N3
  CASP8 MUTATED   14  1  5  0
  CASP8 WILD-TYPE 85 32 94  5
D3V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            14              85
  N1             1              32
  N2             5              94
  N3             0               5
[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, binary
                 cls
clus                0   1
  CASP8 MUTATED    15  12
  CASP8 WILD-TYPE  69 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     15   12
  CASP8 WILD-TYPE   69  210
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            15              69
  MALE              12             210
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     5  22
  CASP8 WILD-TYPE  76 203
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5   22
  CASP8 WILD-TYPE   76  203
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              5              76
  YES            22             203
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED                           1    23
  CASP8 WILD-TYPE                        27   242
D3V10, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    1              27
  WHITE                                       23             242
[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"
D3V11, binary
                 cls
clus                0   1
  CASP8 MUTATED     2  24
  CASP8 WILD-TYPE  12 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      2   24
  CASP8 WILD-TYPE   12  259
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            24             259
[1] 2 2
[1] FALSE

Clustering(4) Variable = FAT1 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    34  22
  FAT1 WILD-TYPE 134  69
  FAT1 MUTATED FAT1 WILD-TYPE 
            56            203 
  FAT1 MUTATED FAT1 WILD-TYPE 
            22             69 
$`FAT1 MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-7872 
         283          276           63          113          236          436 
TCGA-CN-4731 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 
         993         1966         1975          629          594           45 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6222 TCGA-CQ-6223 
         224          611         1660         1253         1407         1057 
TCGA-CR-6477 TCGA-CR-6492 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7382 
         514          479          105           30         1036          796 
TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CV-5430 
        1430          907          898          930          156         1955 
TCGA-CV-5434 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6942 
        3295          519         1478         1970         1952         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7183 
        1948         1966         1959         1970         1936         1979 
TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7435 
        1095         1960         1976         1957         1937         1959 
TCGA-CX-7082 TCGA-CX-7085 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 
         317          321          516          548          299          324 
TCGA-H7-7774 TCGA-HL-7533 
         407         1057 

$`FAT1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BB-4217 TCGA-BB-4223 
         190          644          451          384          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4723 
         423          687          638         1153          428          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1966          683          290          630          933          628 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         629          432           98         1970          202         1110 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          394          735          432          429           46 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 
         317          129         1974         1000          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 
        1959         1179         1007          509         1309         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
        1966         1050         1125         1971         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7383 
        1979          759          889          972         1968         1954 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1951          392          913          946          908 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         216          181         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          406          701         2641 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 
        1948         1969         1959         1969         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         3837         1970         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1987         1952         1444          954          797         1967 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 
        1099         1974         1948         1955         1947         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CX-7086 TCGA-CX-7219 
        1937         1984         1958         1981          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         568         1778         1081         1030         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-F7-7848 TCGA-HD-7229 TCGA-HD-7753 
         775          622          368         1131            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          25           37          485          122          441 

  FAT1 MUTATED FAT1 WILD-TYPE 
            30              2 
  FAT1 MUTATED FAT1 WILD-TYPE 
          3835           3837 
  FAT1 MUTATED FAT1 WILD-TYPE 
         961.5         1000.0 
[1] "30.0 - 3835.0 (961.5)" "2.0 - 3837.0 (1000.0)"
[1] "hr=" "1.2"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FAT1 MUTATED         3       15         8        32         1
  FAT1 WILD-TYPE      14       31        34       117         5
D4V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              3             14
  STAGE II            15             31
  STAGE III            8             34
  STAGE IVA           32            117
  STAGE IVB            1              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  FAT1 MUTATED    3 21 12 23
  FAT1 WILD-TYPE 21 56 51 78
D4V4, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  T1            3             21
  T2           21             56
  T3           12             51
  T4           23             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FAT1 MUTATED   18  7 23  1
  FAT1 WILD-TYPE 81 26 76  4
D4V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           18             81
  N1            7             26
  N2           23             76
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                cls
clus               0   1
  FAT1 MUTATED    25  44
  FAT1 WILD-TYPE  59 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     25   44
  FAT1 WILD-TYPE   59  178
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           25             59
  MALE             44            178
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  FAT1 MUTATED    17  52
  FAT1 WILD-TYPE  64 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     17   52
  FAT1 WILD-TYPE   64  173
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            17             64
  YES           52            173
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  1     2
  FAT1 WILD-TYPE                                0     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           5    56
  FAT1 WILD-TYPE                        23   209
D4V10, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       2              3
  BLACK OR AFRICAN AMERICAN                   5             23
  WHITE                                      56            209
[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"
D4V11, binary
                cls
clus               0   1
  FAT1 MUTATED     6  59
  FAT1 WILD-TYPE   8 224
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      6   59
  FAT1 WILD-TYPE    8  224
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                6              8
  NOT HISPANIC OR LATINO           59            224
[1] 2 2
[1] FALSE

Clustering(5) Variable = MLL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    26  22
  MLL2 WILD-TYPE 142  69
  MLL2 MUTATED MLL2 WILD-TYPE 
            48            211 
  MLL2 MUTATED MLL2 WILD-TYPE 
            22             69 
$`MLL2 MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5558 
         462          283          415         1983          248         1636 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-CN-4731 
         451           63          536          638         1153          993 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-5370 TCGA-CN-6011 TCGA-CN-6021 
        1250          625         1268         1975          933         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6996 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-6221 
         202         1110          432          429         1466         1000 
TCGA-CR-5243 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7379 
        2562         1125         1969          354          234         1036 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7402 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 
        1951          392          911         3295          584         2886 
TCGA-CV-6441 TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 
        1970         1979         1967         1976         1099         1957 
TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CX-7086 TCGA-HD-7917 TCGA-IQ-7632 
        1972         1958         1959          237           37          441 

$`MLL2 WILD-TYPE`
TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         276          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
         623         1747          190          644          384          113 
TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         236          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
         558          310          423          687          428          436 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721         1157          142         1230         1151          392 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
         817          642          758          395         1960         1330 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1988         1007         1045          173         1980 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1081         1681         1977         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         683          290          630          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 
         629           45          432           98          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 TCGA-CQ-5324 TCGA-CQ-5325 
         611          394          735           46         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
        1660         1422         1393         1399          317          129 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
        1253         1974         1407         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5247 
        1959         1179         1007          509         1309          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1971          514          362          311          345 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 
         889           30          972         1968          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 
        1472         1955          522         1950         1438          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1665          641         1899         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 
        1936         1959         1939         1945         1987         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7406 
        1444         1095          954          797         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7433 
        1948         1955         1947         1937         1937         1984 
TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1981          317          321          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 
         701           77          491          154          568         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1081          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HL-7533 TCGA-IQ-7630 
         407            2            5           25         1057          485 
TCGA-IQ-7631 
         122 

  MLL2 MUTATED MLL2 WILD-TYPE 
            37              2 
  MLL2 MUTATED MLL2 WILD-TYPE 
          3295           3837 
  MLL2 MUTATED MLL2 WILD-TYPE 
        1067.5          972.0 
[1] "37.0 - 3295.0 (1067.5)" "2.0 - 3837.0 (972.0)"  
[1] "hr=" "1"  
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MLL2 MUTATED         2        4         5        29         0
  MLL2 WILD-TYPE      15       42        37       120         6
D5V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I              2             15
  STAGE II             4             42
  STAGE III            5             37
  STAGE IVA           29            120
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MLL2 MUTATED    2  7 14 18
  MLL2 WILD-TYPE 22 70 49 83
D5V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            2             22
  T2            7             70
  T3           14             49
  T4           18             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   15  5 18  0
  MLL2 WILD-TYPE 84 28 81  5
D5V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           15             84
  N1            5             28
  N2           18             81
  N3            0              5
[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, binary
                cls
clus               0   1
  MLL2 MUTATED    15  38
  MLL2 WILD-TYPE  69 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     15   38
  MLL2 WILD-TYPE   69  184
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           15             69
  MALE             38            184
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  MLL2 MUTATED    14  39
  MLL2 WILD-TYPE  67 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     14   39
  MLL2 WILD-TYPE   67  186
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            14             67
  YES           39            186
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  0     1
  MLL2 WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED                           7    43
  MLL2 WILD-TYPE                        21   222
D5V10, multiclass
                                  clus
vv                                 MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              4
  BLACK OR AFRICAN AMERICAN                   7             21
  WHITE                                      43            222
[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"
D5V11, binary
                cls
clus               0   1
  MLL2 MUTATED     2  49
  MLL2 WILD-TYPE  12 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   49
  MLL2 WILD-TYPE   12  234
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             12
  NOT HISPANIC OR LATINO           49            234
[1] 2 2
[1] FALSE

Clustering(6) Variable = JUB MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  JUB MUTATED     7   9
  JUB WILD-TYPE 161  82
  JUB MUTATED JUB WILD-TYPE 
           16           243 
  JUB MUTATED JUB WILD-TYPE 
            9            82 
$`JUB MUTATED`
TCGA-BA-5556 TCGA-CN-4738 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5327 TCGA-CR-6491 
         725         1960          429           46         1660          350 
TCGA-CR-6493 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-6003 TCGA-CV-7099 TCGA-CV-7418 
        1956          522         1438         1665         1936         1955 
TCGA-CV-7432 TCGA-CX-7082 TCGA-DQ-7588 TCGA-HD-7753 
        1937          317         1965            5 

$`JUB WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          520          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         113          236          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 
         638         1153          428          436          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 
         642          758         1250          395          625         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1980         1081         1681         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CQ-5323 TCGA-CQ-5324 
         611          394          735          432         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
         654         1422         1393         1399          317          129 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
        1253         1974         1000         1407         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1007          509         1309 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         379          479         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472         1955         1950         3295 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1970         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1987         1979         1952         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1948         1957         1947         1937         1972         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1958         1959         1981          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         568         1778         1081          516         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          299          368          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
        1131          407            2           25           37         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         485          122          441 

  JUB MUTATED JUB WILD-TYPE 
            5             2 
  JUB MUTATED JUB WILD-TYPE 
         1965          3837 
  JUB MUTATED JUB WILD-TYPE 
         1549           993 
[1] "5.0 - 1965.0 (1549.0)" "2.0 - 3837.0 (993.0)" 
[1] "hr=" "2.9"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  JUB MUTATED         1        4         1        11         0
  JUB WILD-TYPE      16       42        41       138         6
D6V3, multiclass
           clus
vv          JUB MUTATED JUB WILD-TYPE
  STAGE I             1            16
  STAGE II            4            42
  STAGE III           1            41
  STAGE IVA          11           138
  STAGE IVB           0             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  JUB MUTATED    1  6  6  4
  JUB WILD-TYPE 23 71 57 97
D6V4, multiclass
    clus
vv   JUB MUTATED JUB WILD-TYPE
  T1           1            23
  T2           6            71
  T3           6            57
  T4           4            97
[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"
               vv
clus            N0 N1 N2 N3
  JUB MUTATED    4  1 10  0
  JUB WILD-TYPE 95 32 89  5
D6V5, multiclass
    clus
vv   JUB MUTATED JUB WILD-TYPE
  N0           4            95
  N1           1            32
  N2          10            89
  N3           0             5
[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, binary
               cls
clus              0   1
  JUB MUTATED     5  13
  JUB WILD-TYPE  79 209
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      5   13
  JUB WILD-TYPE   79  209
        clus
vv       JUB MUTATED JUB WILD-TYPE
  FEMALE           5            79
  MALE            13           209
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus              0   1
  JUB MUTATED     5  13
  JUB WILD-TYPE  76 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      5   13
  JUB WILD-TYPE   76  212
     clus
vv    JUB MUTATED JUB WILD-TYPE
  NO            5            76
  YES          13           212
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JUB MUTATED                                  0     1
  JUB WILD-TYPE                                1     4
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  JUB MUTATED                           4    13
  JUB WILD-TYPE                        24   252
D6V10, multiclass
                                  clus
vv                                 JUB MUTATED JUB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             4
  BLACK OR AFRICAN AMERICAN                  4            24
  WHITE                                     13           252
[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"
D6V11, binary
               cls
clus              0   1
  JUB MUTATED     1  16
  JUB WILD-TYPE  13 267
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      1   16
  JUB WILD-TYPE   13  267
                        clus
vv                       JUB MUTATED JUB WILD-TYPE
  HISPANIC OR LATINO               1            13
  NOT HISPANIC OR LATINO          16           267
[1] 2 2
[1] FALSE

Clustering(7) Variable = NOTCH1 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    27  20
  NOTCH1 WILD-TYPE 141  71
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              47              212 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              20               71 
$`NOTCH1 MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6873 TCGA-BB-4225 
         283          415          248          190          113          140 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4736 
         423          687          436          721          392          395 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6021 
        1988         1007         1977          933          594         1970 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CR-5243 
         611          735         1422          129         1974         2562 
TCGA-CR-7365 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7394 
        1191          972         1968         1036          907          898 
TCGA-CR-7395 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5971 
         930          584          546         2886          519          701 
TCGA-CV-5973 TCGA-CV-6942 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7238 TCGA-CV-7410 
        2641         3835         1936         1939         1444         1948 
TCGA-CV-7427 TCGA-CV-7433 TCGA-CX-7085 TCGA-DQ-5625 TCGA-DQ-5631 
        1937         1984          321         1081          548 

$`NOTCH1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462         1983          276          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 
         451           63          384          236          187         2878 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
         278          133          558          310          536          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        1153          428         1157          142         1230         1151 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 
         817          993          642          758         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
        1960         1330          811         1268         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1681         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
        1975          683          290          630          629          628 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
         629           45          432           98          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         224          318          394          432          429           46 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1660         1393         1399 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
         317         1253         1000         1407         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1007          509         1309 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         913          946          908          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
        3295         1438         1978         2327         1958         2437 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         406         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1959         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        1959         3837         1959         1970         1970         1959 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 
        1945         1987         1979         1952         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        1955         1957         1947         1972         1937         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1959         1981          317          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
        1778          516         1030         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 
         622          299          368          324         1131          407 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 
           2            5           25           37         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 
         122          441 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
             113                2 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            3835             3837 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           907.0           1037.5 
[1] "113.0 - 3835.0 (907.0)" "2.0 - 3837.0 (1037.5)" 
[1] "hr=" "1.1"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NOTCH1 MUTATED         2        9         8        28         2
  NOTCH1 WILD-TYPE      15       37        34       121         4
D7V3, multiclass
           clus
vv          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                2               15
  STAGE II               9               37
  STAGE III              8               34
  STAGE IVA             28              121
  STAGE IVB              2                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  NOTCH1 MUTATED    3 13 12 22
  NOTCH1 WILD-TYPE 21 64 51 79
D7V4, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T1              3               21
  T2             13               64
  T3             12               51
  T4             22               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NOTCH1 MUTATED   19  6 16  1
  NOTCH1 WILD-TYPE 80 27 83  4
D7V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0             19               80
  N1              6               27
  N2             16               83
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    20  37
  NOTCH1 WILD-TYPE  64 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     20   37
  NOTCH1 WILD-TYPE   64  185
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             20               64
  MALE               37              185
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    12  45
  NOTCH1 WILD-TYPE  69 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     12   45
  NOTCH1 WILD-TYPE   69  180
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              12               69
  YES             45              180
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH1 MUTATED                                  0     1
  NOTCH1 WILD-TYPE                                1     4
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED                           4    49
  NOTCH1 WILD-TYPE                        24   216
D7V10, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                4
  BLACK OR AFRICAN AMERICAN                     4               24
  WHITE                                        49              216
[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"
D7V11, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     5  51
  NOTCH1 WILD-TYPE   9 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      5   51
  NOTCH1 WILD-TYPE    9  232
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  5                9
  NOT HISPANIC OR LATINO             51              232
[1] 2 2
[1] FALSE

Clustering(8) Variable = NFE2L2 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     6   5
  NFE2L2 WILD-TYPE 162  86
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              248 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               5               86 
$`NFE2L2 MUTATED`
TCGA-BA-7269 TCGA-CN-4723 TCGA-CN-6019 TCGA-CQ-5324 TCGA-CR-7383 TCGA-CV-6935 
         236          721          432         1207         1954         1969 
TCGA-CV-6942 TCGA-CV-7099 TCGA-CV-7424 TCGA-CV-7433 TCGA-H7-7774 
        3835         1936         1947         1984          407 

$`NFE2L2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         384          113          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4725 TCGA-CN-4726 
         638         1153          428          436         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         758         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1980         1081         1681         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
         629          628          594          629           45           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
         394          735          432          429           46         1466 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 
         129         1253         1974         1000         1407         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959         1959         1179         1007          509 
TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
        1309         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1952         1959         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         1957 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1937         1972         1937         1958         1959         1981 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 
         701           77          491          154          568         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1081          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 
           2            5           25           37         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 
         122          441 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
             236                2 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            3835             3837 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1936              989 
[1] "236.0 - 3835.0 (1936.0)" "2.0 - 3837.0 (989.0)"   
[1] "hr=" "1.3"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NFE2L2 MUTATED         1        5         3         8         0
  NFE2L2 WILD-TYPE      16       41        39       141         6
D8V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                1               16
  STAGE II               5               41
  STAGE III              3               39
  STAGE IVA              8              141
  STAGE IVB              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  NFE2L2 MUTATED    1  7  3  6
  NFE2L2 WILD-TYPE 23 70 60 95
D8V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              1               23
  T2              7               70
  T3              3               60
  T4              6               95
[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"
                  vv
clus               N0 N1 N2 N3
  NFE2L2 MUTATED    5  2  5  0
  NFE2L2 WILD-TYPE 94 31 94  5
D8V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              5               94
  N1              2               31
  N2              5               94
  N3              0                5
[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, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     7  10
  NFE2L2 WILD-TYPE  77 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      7   10
  NFE2L2 WILD-TYPE   77  212
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              7               77
  MALE               10              212
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  15
  NFE2L2 WILD-TYPE  79 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   15
  NFE2L2 WILD-TYPE   79  210
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               2               79
  YES             15              210
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                1     4
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           0    14
  NFE2L2 WILD-TYPE                        28   251
D8V10, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                4
  BLACK OR AFRICAN AMERICAN                     0               28
  WHITE                                        14              251
[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"
D8V11, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     1  14
  NFE2L2 WILD-TYPE  13 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      1   14
  NFE2L2 WILD-TYPE   13  269
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO             14              269
[1] 2 2
[1] FALSE

Clustering(9) Variable = NSD1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  NSD1 MUTATED    23   7
  NSD1 WILD-TYPE 145  84
  NSD1 MUTATED NSD1 WILD-TYPE 
            30            229 
  NSD1 MUTATED NSD1 WILD-TYPE 
             7             84 
$`NSD1 MUTATED`
TCGA-BA-5555 TCGA-BA-6869 TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4739 
         520          644         1153         1230          817         1330 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CR-5247 TCGA-CR-6481 TCGA-CR-7364 TCGA-CR-7385 
        1045         1081          358          311         1435          997 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6441 
         930          156          911         2886         1665         1970 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7242 TCGA-CV-7245 
        1959         3835         1969         1959         1095          797 
TCGA-CV-7250 TCGA-CV-7427 TCGA-CV-7440 TCGA-DQ-7595 TCGA-F7-7848 TCGA-HD-7917 
        1960         1937         1981          324         1131           37 

$`NSD1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1747          190          451           63          384          113 
TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         236          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
         428          436          721         1157          142         1151 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
         392          993          642          758         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         625         1960          811         1268         1988         1007 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1681         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1399          317          129         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
        1007          509         1309         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
        1971          514         1969          362          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
         234          379          350          479         1956         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
        1954         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
         946          908          898          216          181         1077 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         1978         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
         215         1315          641         1899         1948         1969 
TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-7090 
        1952         1948         1969         1966         1957         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1945         1987         1979         1952         1444          954 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1957         1947         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1959          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-H7-7774 
         575          775          622          299          368          407 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
           2            5           25         1057          485          122 
TCGA-IQ-7632 
         441 

  NSD1 MUTATED NSD1 WILD-TYPE 
            37              2 
  NSD1 MUTATED NSD1 WILD-TYPE 
          3835           3837 
  NSD1 MUTATED NSD1 WILD-TYPE 
          1113            954 
[1] "37.0 - 3835.0 (1113.0)" "2.0 - 3837.0 (954.0)"  
[1] "hr=" "1.9"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NSD1 MUTATED         0        8         8        11         1
  NSD1 WILD-TYPE      17       38        34       138         5
D9V3, multiclass
           clus
vv          NSD1 MUTATED NSD1 WILD-TYPE
  STAGE I              0             17
  STAGE II             8             38
  STAGE III            8             34
  STAGE IVA           11            138
  STAGE IVB            1              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  NSD1 MUTATED    1  9  8 11
  NSD1 WILD-TYPE 23 68 55 90
D9V4, multiclass
    clus
vv   NSD1 MUTATED NSD1 WILD-TYPE
  T1            1             23
  T2            9             68
  T3            8             55
  T4           11             90
[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"
                vv
clus             N0 N1 N2 N3
  NSD1 MUTATED   18  4  2  1
  NSD1 WILD-TYPE 81 29 97  4
D9V5, multiclass
    clus
vv   NSD1 MUTATED NSD1 WILD-TYPE
  N0           18             81
  N1            4             29
  N2            2             97
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                cls
clus               0   1
  NSD1 MUTATED     6  27
  NSD1 WILD-TYPE  78 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      6   27
  NSD1 WILD-TYPE   78  195
        clus
vv       NSD1 MUTATED NSD1 WILD-TYPE
  FEMALE            6             78
  MALE             27            195
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  NSD1 MUTATED     6  27
  NSD1 WILD-TYPE  75 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      6   27
  NSD1 WILD-TYPE   75  198
     clus
vv    NSD1 MUTATED NSD1 WILD-TYPE
  NO             6             75
  YES           27            198
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSD1 MUTATED                                  0     0
  NSD1 WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NSD1 MUTATED                           5    26
  NSD1 WILD-TYPE                        23   239
D9V10, multiclass
                                  clus
vv                                 NSD1 MUTATED NSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              5
  BLACK OR AFRICAN AMERICAN                   5             23
  WHITE                                      26            239
[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"
D9V11, binary
                cls
clus               0   1
  NSD1 MUTATED     4  28
  NSD1 WILD-TYPE  10 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      4   28
  NSD1 WILD-TYPE   10  255
                        clus
vv                       NSD1 MUTATED NSD1 WILD-TYPE
  HISPANIC OR LATINO                4             10
  NOT HISPANIC OR LATINO           28            255
[1] 2 2
[1] FALSE

Clustering(10) Variable = HRAS MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     8   1
  HRAS WILD-TYPE 160  90
  HRAS MUTATED HRAS WILD-TYPE 
             9            250 
  HRAS MUTATED HRAS WILD-TYPE 
             1             90 
$`HRAS MUTATED`
TCGA-BA-5556 TCGA-CQ-5324 TCGA-CQ-7068 TCGA-CR-7382 TCGA-CR-7394 TCGA-CR-7395 
         725         1207         1309          796          898          930 
TCGA-CV-6436 TCGA-CV-7183 TCGA-CV-7250 
        1899         1979         1960 

$`HRAS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          520          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         113          236          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 
         638         1153          428          436          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
          46         1466          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1399          317          129         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
        1007          509         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 
         907          913          946          908          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1665          641         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 
        1936         1959         1939         1945         1987         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1444         1095          954          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1981          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          299          368          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
        1131          407            2            5           25           37 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        1057          485          122          441 

  HRAS MUTATED HRAS WILD-TYPE 
           725              2 
  HRAS MUTATED HRAS WILD-TYPE 
          1979           3837 
  HRAS MUTATED HRAS WILD-TYPE 
          1207            995 
[1] "725.0 - 1979.0 (1207.0)" "2.0 - 3837.0 (995.0)"   
[1] "hr=" "3.2"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HRAS MUTATED         0        5         1         4         0
  HRAS WILD-TYPE      17       41        41       145         6
D10V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              0             17
  STAGE II             5             41
  STAGE III            1             41
  STAGE IVA            4            145
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  HRAS MUTATED    0  6  1  3
  HRAS WILD-TYPE 24 71 62 98
D10V4, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T1            0             24
  T2            6             71
  T3            1             62
  T4            3             98
[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"
                vv
clus             N0 N1 N2 N3
  HRAS MUTATED    8  0  1  0
  HRAS WILD-TYPE 91 33 98  5
D10V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0            8             91
  N1            0             33
  N2            1             98
  N3            0              5
[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, binary
                cls
clus               0   1
  HRAS MUTATED     3   7
  HRAS WILD-TYPE  81 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      3    7
  HRAS WILD-TYPE   81  215
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            3             81
  MALE              7            215
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus               0   1
  HRAS MUTATED     1   9
  HRAS WILD-TYPE  80 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1    9
  HRAS WILD-TYPE   80  216
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             1             80
  YES            9            216
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     0
  HRAS WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           0    10
  HRAS WILD-TYPE                        28   255
D10V10, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              5
  BLACK OR AFRICAN AMERICAN                   0             28
  WHITE                                      10            255
[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"
D10V11, binary
                cls
clus               0   1
  HRAS MUTATED     0  10
  HRAS WILD-TYPE  14 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   10
  HRAS WILD-TYPE   14  273
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO           10            273
[1] 2 2
[1] FALSE

Clustering(11) Variable = ZNF750 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED     7   4
  ZNF750 WILD-TYPE 161  87
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              11              248 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               4               87 
$`ZNF750 MUTATED`
TCGA-BB-7870 TCGA-CR-6481 TCGA-CR-7368 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5444 
        1153          311         1245         1472         3295         2437 
TCGA-CV-6961 TCGA-CV-7418 TCGA-DQ-5629 TCGA-DQ-7594 TCGA-HL-7533 
        1959         1955          516          368         1057 

$`ZNF750 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 
         687          638          428          436          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
          46         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
        1956         1435         1191         1440         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955          522         1950         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
        1978         2886         2327         1958          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1960         1976         1099         1974         1948         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1959         1981          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         568         1778         1081         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 
         575          775          622          299          324         1131 
TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-IQ-7630 
         407            2            5           25           37          485 
TCGA-IQ-7631 TCGA-IQ-7632 
         122          441 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
             311                2 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
            3295             3837 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
          1245.0            978.5 
[1] "311.0 - 3295.0 (1245.0)" "2.0 - 3837.0 (978.5)"   
[1] "hr=" "1.6"
D11V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ZNF750 MUTATED         0        1         0         7         0
  ZNF750 WILD-TYPE      17       45        42       142         6
D11V3, multiclass
           clus
vv          ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                0               17
  STAGE II               1               45
  STAGE III              0               42
  STAGE IVA              7              142
  STAGE IVB              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ZNF750 MUTATED    0  1  0  7
  ZNF750 WILD-TYPE 24 76 63 94
D11V4, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  T1              0               24
  T2              1               76
  T3              0               63
  T4              7               94
[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"
                  vv
clus               N0 N1 N2 N3
  ZNF750 MUTATED    3  2  3  0
  ZNF750 WILD-TYPE 96 31 96  5
D11V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              3               96
  N1              2               31
  N2              3               96
  N3              0                5
[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, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     1  12
  ZNF750 WILD-TYPE  83 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      1   12
  ZNF750 WILD-TYPE   83  210
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              1               83
  MALE               12              210
[1] 2 2
[1] FALSE
D11V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     2  11
  ZNF750 WILD-TYPE  79 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2   11
  ZNF750 WILD-TYPE   79  214
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               2               79
  YES             11              214
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF750 MUTATED                                  0     0
  ZNF750 WILD-TYPE                                1     5
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF750 MUTATED                           3    10
  ZNF750 WILD-TYPE                        25   255
D11V10, multiclass
                                  clus
vv                                 ZNF750 MUTATED ZNF750 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                5
  BLACK OR AFRICAN AMERICAN                     3               25
  WHITE                                        10              255
[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"
D11V11, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     0  13
  ZNF750 WILD-TYPE  14 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   13
  ZNF750 WILD-TYPE   14  270
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO             13              270
[1] 2 2
[1] FALSE

Clustering(12) Variable = RASA1 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED     7   3
  RASA1 WILD-TYPE 161  88
  RASA1 MUTATED RASA1 WILD-TYPE 
             10             249 
  RASA1 MUTATED RASA1 WILD-TYPE 
              3              88 
$`RASA1 MUTATED`
TCGA-CN-4723 TCGA-CN-5366 TCGA-CN-6023 TCGA-CQ-6219 TCGA-CQ-6224 TCGA-CR-6492 
         721         1966         1110         1974          985          479 
TCGA-CR-7365 TCGA-CV-7243 TCGA-DQ-5629 TCGA-IQ-7630 
        1191          954          516          485 

$`RASA1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4725 
         687          638         1153          428          436         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98         1970          202          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
         394          735          432          429           46         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 
         317          129         1253         1000         1407         1057 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1007          509         1309 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         379          350         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1952         1444         1095          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1959         1981          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         568         1778         1081         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          299          368          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
        1131          407            2            5           25           37 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
        1057          122          441 

  RASA1 MUTATED RASA1 WILD-TYPE 
            479               2 
  RASA1 MUTATED RASA1 WILD-TYPE 
           1974            3837 
  RASA1 MUTATED RASA1 WILD-TYPE 
          969.5          1000.0 
[1] "479.0 - 1974.0 (969.5)" "2.0 - 3837.0 (1000.0)" 
[1] "hr=" "1"  
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RASA1 MUTATED         0        2         3         8         0
  RASA1 WILD-TYPE      17       44        39       141         6
D12V3, multiclass
           clus
vv          RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I               0              17
  STAGE II              2              44
  STAGE III             3              39
  STAGE IVA             8             141
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  RASA1 MUTATED    0  6  3  4
  RASA1 WILD-TYPE 24 71 60 97
D12V4, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  T1             0              24
  T2             6              71
  T3             3              60
  T4             4              97
[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"
                 vv
clus              N0 N1 N2 N3
  RASA1 MUTATED    5  2  6  0
  RASA1 WILD-TYPE 94 31 93  5
D12V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             5              94
  N1             2              31
  N2             6              93
  N3             0               5
[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, binary
                 cls
clus                0   1
  RASA1 MUTATED     2  12
  RASA1 WILD-TYPE  82 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      2   12
  RASA1 WILD-TYPE   82  210
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE             2              82
  MALE              12             210
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  RASA1 MUTATED     5   9
  RASA1 WILD-TYPE  76 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      5    9
  RASA1 WILD-TYPE   76  216
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              5              76
  YES             9             216
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA1 MUTATED                                  0     0
  RASA1 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA1 MUTATED                           0    14
  RASA1 WILD-TYPE                        28   251
D12V10, multiclass
                                  clus
vv                                 RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               5
  BLACK OR AFRICAN AMERICAN                    0              28
  WHITE                                       14             251
[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"
D12V11, binary
                 cls
clus                0   1
  RASA1 MUTATED     1  13
  RASA1 WILD-TYPE  13 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      1   13
  RASA1 WILD-TYPE   13  270
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO            13             270
[1] 2 2
[1] FALSE

Clustering(13) Variable = HLA-A MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED     5   3
  HLA-A WILD-TYPE 163  88
  HLA-A MUTATED HLA-A WILD-TYPE 
              8             251 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              88 
$`HLA-A MUTATED`
TCGA-BA-5152 TCGA-BA-6868 TCGA-CR-6467 TCGA-CR-7373 TCGA-CR-7395 TCGA-CV-5976 
        1288          190         1777          889          930         1478 
TCGA-CV-6943 TCGA-CV-7099 
        1948         1936 

$`HLA-A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1747          644          451           63          384          113 
TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         236          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        1153          428          436          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         758         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1980         1081         1681         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1399          317          129         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          759           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
         907          913          946          908          898          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1952         1959         3835         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1959         1981          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         568         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1965          575          775          622          299          368 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         324         1131          407            2            5           25 
TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          37         1057          485          122          441 

  HLA-A MUTATED HLA-A WILD-TYPE 
            190               2 
  HLA-A MUTATED HLA-A WILD-TYPE 
           1948            3837 
  HLA-A MUTATED HLA-A WILD-TYPE 
           1383             993 
[1] "190.0 - 1948.0 (1383.0)" "2.0 - 3837.0 (993.0)"   
[1] "hr=" "2.4"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HLA-A MUTATED         0        3         2         3         0
  HLA-A WILD-TYPE      17       43        40       146         6
D13V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0              17
  STAGE II              3              43
  STAGE III             2              40
  STAGE IVA             3             146
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  HLA-A MUTATED    0  4  1  3
  HLA-A WILD-TYPE 24 73 62 98
D13V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0              24
  T2             4              73
  T3             1              62
  T4             3              98
[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"
                 vv
clus              N0 N1 N2 N3
  HLA-A MUTATED    3  2  1  0
  HLA-A WILD-TYPE 96 31 98  5
D13V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             3              96
  N1             2              31
  N2             1              98
  N3             0               5
[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, binary
                 cls
clus                0   1
  HLA-A MUTATED     2   7
  HLA-A WILD-TYPE  82 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      2    7
  HLA-A WILD-TYPE   82  215
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             2              82
  MALE               7             215
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     3   6
  HLA-A WILD-TYPE  78 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3    6
  HLA-A WILD-TYPE   78  219
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              3              78
  YES             6             219
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  0     0
  HLA-A WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED                           1     8
  HLA-A WILD-TYPE                        27   257
D13V10, multiclass
                                  clus
vv                                 HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               5
  BLACK OR AFRICAN AMERICAN                    1              27
  WHITE                                        8             257
[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"
D13V11, binary
                 cls
clus                0   1
  HLA-A MUTATED     0   8
  HLA-A WILD-TYPE  14 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0    8
  HLA-A WILD-TYPE   14  275
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             8             275
[1] 2 2
[1] FALSE

Clustering(14) Variable = EPHA2 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED     5   4
  EPHA2 WILD-TYPE 163  87
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              9             250 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              4              87 
$`EPHA2 MUTATED`
TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-6873 TCGA-CN-4726 TCGA-CN-4734 TCGA-CN-5355 
        1983         1288          113          142          758         1007 
TCGA-CQ-5327 TCGA-CQ-5334 TCGA-CV-7440 
        1660          129         1981 

$`EPHA2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
         190          644          451           63          384          236 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 
         428          436          721         1157         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
        1045          173         1980         1081         1681         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
         429           46         1466         1207          654         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1393         1399          317         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1899         1970         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1959          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          299          368          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
        1131          407            2            5           25           37 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        1057          485          122          441 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
            113               2 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
           1983            3837 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
           1007             995 
[1] "113.0 - 1983.0 (1007.0)" "2.0 - 3837.0 (995.0)"   
[1] "hr=" "1"  
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EPHA2 MUTATED         1        2         1         9         0
  EPHA2 WILD-TYPE      16       44        41       140         6
D14V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               1              16
  STAGE II              2              44
  STAGE III             1              41
  STAGE IVA             9             140
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  EPHA2 MUTATED    1  3  4  5
  EPHA2 WILD-TYPE 23 74 59 96
D14V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             1              23
  T2             3              74
  T3             4              59
  T4             5              96
[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"
                 vv
clus              N0 N1 N2 N3
  EPHA2 MUTATED    5  0  5  0
  EPHA2 WILD-TYPE 94 33 94  5
D14V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             5              94
  N1             0              33
  N2             5              94
  N3             0               5
[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, binary
                 cls
clus                0   1
  EPHA2 MUTATED     6   7
  EPHA2 WILD-TYPE  78 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      6    7
  EPHA2 WILD-TYPE   78  215
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             6              78
  MALE               7             215
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     3  10
  EPHA2 WILD-TYPE  78 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      3   10
  EPHA2 WILD-TYPE   78  215
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              3              78
  YES            10             215
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA2 MUTATED                                  0     1
  EPHA2 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED                           2     9
  EPHA2 WILD-TYPE                        26   256
D14V10, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    2              26
  WHITE                                        9             256
[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"
D14V11, binary
                 cls
clus                0   1
  EPHA2 MUTATED     1  12
  EPHA2 WILD-TYPE  13 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      1   12
  EPHA2 WILD-TYPE   13  271
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO            12             271
[1] 2 2
[1] FALSE

Clustering(15) Variable = RAC1 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     5   3
  RAC1 WILD-TYPE 163  88
  RAC1 MUTATED RAC1 WILD-TYPE 
             8            251 
  RAC1 MUTATED RAC1 WILD-TYPE 
             3             88 
$`RAC1 MUTATED`
TCGA-BA-4078 TCGA-CQ-6223 TCGA-CR-5250 TCGA-CR-7367 TCGA-CR-7388 TCGA-CV-7427 
         276         1057          799         1440         1951         1937 
TCGA-CX-7085 TCGA-H7-7774 
         321          407 

$`RAC1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         113          236          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 
         638         1153          428          436          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
          46         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1407          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1191         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1430          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1987         1979         1952         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 
        1948         1955         1957         1947         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7086 
        1984         1958         1959         1981          317          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         154          568         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         368          324         1131            2            5           25 
TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          37         1057          485          122          441 

  RAC1 MUTATED RAC1 WILD-TYPE 
           276              2 
  RAC1 MUTATED RAC1 WILD-TYPE 
          1951           3837 
  RAC1 MUTATED RAC1 WILD-TYPE 
           928            997 
[1] "276.0 - 1951.0 (928.0)" "2.0 - 3837.0 (997.0)"  
[1] "hr=" "2.6"
D15V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RAC1 MUTATED         1        2         0         3         0
  RAC1 WILD-TYPE      16       44        42       146         6
D15V3, multiclass
           clus
vv          RAC1 MUTATED RAC1 WILD-TYPE
  STAGE I              1             16
  STAGE II             2             44
  STAGE III            0             42
  STAGE IVA            3            146
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  RAC1 MUTATED    1  2  0  3
  RAC1 WILD-TYPE 23 75 63 98
D15V4, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  T1            1             23
  T2            2             75
  T3            0             63
  T4            3             98
[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"
                vv
clus             N0 N1 N2 N3
  RAC1 MUTATED    4  1  0  0
  RAC1 WILD-TYPE 95 32 99  5
D15V5, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            4             95
  N1            1             32
  N2            0             99
  N3            0              5
[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, binary
                cls
clus               0   1
  RAC1 MUTATED     5   4
  RAC1 WILD-TYPE  79 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      5    4
  RAC1 WILD-TYPE   79  218
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            5             79
  MALE              4            218
[1] 2 2
[1] FALSE
D15V7, binary
                cls
clus               0   1
  RAC1 MUTATED     2   7
  RAC1 WILD-TYPE  79 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      2    7
  RAC1 WILD-TYPE   79  218
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             2             79
  YES            7            218
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAC1 MUTATED                                  0     0
  RAC1 WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED                           0     9
  RAC1 WILD-TYPE                        28   256
D15V10, multiclass
                                  clus
vv                                 RAC1 MUTATED RAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              5
  BLACK OR AFRICAN AMERICAN                   0             28
  WHITE                                       9            256
[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"
D15V11, binary
                cls
clus               0   1
  RAC1 MUTATED     0   9
  RAC1 WILD-TYPE  14 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0    9
  RAC1 WILD-TYPE   14  274
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            9            274
[1] 2 2
[1] FALSE

Clustering(16) Variable = EP300 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    13   8
  EP300 WILD-TYPE 155  83
  EP300 MUTATED EP300 WILD-TYPE 
             21             238 
  EP300 MUTATED EP300 WILD-TYPE 
              8              83 
$`EP300 MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5559 TCGA-BB-7863 TCGA-BB-7870 TCGA-CQ-5327 
         283          415         1747          423         1153         1660 
TCGA-CQ-5331 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6487 TCGA-CR-7394 TCGA-CR-7395 
        1399         1521         1966          234          898          930 
TCGA-CV-5434 TCGA-CV-6943 TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7427 TCGA-CX-7219 
        3295         1948         1970         1959         1937          828 
TCGA-D6-6516 TCGA-DQ-7595 TCGA-H7-7774 
         773          324          407 

$`EP300 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462         1983          276          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1762          520          725          623         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
         310          536          687          638          428          436 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721         1157          142         1230         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
         817          993          642          758         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
        1007         1045          173         1980         1081         1681 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1110          224          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         432          429           46         1466         1207          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1422         1393          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6472 TCGA-CR-6473 
        1663         1152          799         1777         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 
         907          913          946          908          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1959         3835         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 
        1959         3837         1959         1970         1936         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 
        1974         1948         1955         1957         1947         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 
        1937         1984         1958         1959         1981          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         321          237          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         154          568         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-F7-7848 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         368         1131            2            5           25           37 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        1057          485          122          441 

  EP300 MUTATED EP300 WILD-TYPE 
            234               2 
  EP300 MUTATED EP300 WILD-TYPE 
           3295            3837 
  EP300 MUTATED EP300 WILD-TYPE 
           1153             995 
[1] "234.0 - 3295.0 (1153.0)" "2.0 - 3837.0 (995.0)"   
[1] "hr=" "1.2"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EP300 MUTATED         2        5         4         9         0
  EP300 WILD-TYPE      15       41        38       140         6
D16V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               2              15
  STAGE II              5              41
  STAGE III             4              38
  STAGE IVA             9             140
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  EP300 MUTATED    2  7  4  8
  EP300 WILD-TYPE 22 70 59 93
D16V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             2              22
  T2             7              70
  T3             4              59
  T4             8              93
[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"
                 vv
clus              N0 N1 N2 N3
  EP300 MUTATED    9  2  5  0
  EP300 WILD-TYPE 90 31 94  5
D16V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0             9              90
  N1             2              31
  N2             5              94
  N3             0               5
[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, binary
                 cls
clus                0   1
  EP300 MUTATED     8  16
  EP300 WILD-TYPE  76 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      8   16
  EP300 WILD-TYPE   76  206
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE             8              76
  MALE              16             206
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  EP300 MUTATED     5  19
  EP300 WILD-TYPE  76 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      5   19
  EP300 WILD-TYPE   76  206
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              5              76
  YES            19             206
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     1
  EP300 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED                           3    19
  EP300 WILD-TYPE                        25   246
D16V10, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    3              25
  WHITE                                       19             246
[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"
D16V11, binary
                 cls
clus                0   1
  EP300 MUTATED     2  21
  EP300 WILD-TYPE  12 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   21
  EP300 WILD-TYPE   12  262
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO            21             262
[1] 2 2
[1] FALSE

Clustering(17) Variable = TGFBR2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED     4   3
  TGFBR2 WILD-TYPE 164  88
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               7              252 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               3               88 
$`TGFBR2 MUTATED`
TCGA-CN-4731 TCGA-CR-7376 TCGA-CR-7402 TCGA-CV-5444 TCGA-CV-6943 TCGA-CV-6954 
         993          972          911         2437         1948         1957 
TCGA-CV-6961 
        1959 

$`TGFBR2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
          46         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         215         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        1948         1969         1952         1959         3835         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1966         1969         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1958         1959         1981          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         154          568         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 
         368          324         1131          407            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          25           37         1057          485          122          441 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
             911                2 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            2437             3837 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1948              991 
[1] "911.0 - 2437.0 (1948.0)" "2.0 - 3837.0 (991.0)"   
[1] "hr=" "1.2"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TGFBR2 MUTATED         0        2         2         5         0
  TGFBR2 WILD-TYPE      17       44        40       144         6
D17V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                0               17
  STAGE II               2               44
  STAGE III              2               40
  STAGE IVA              5              144
  STAGE IVB              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  TGFBR2 MUTATED    0  3  1  5
  TGFBR2 WILD-TYPE 24 74 62 96
D17V4, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1              0               24
  T2              3               74
  T3              1               62
  T4              5               96
[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"
                  vv
clus               N0 N1 N2 N3
  TGFBR2 MUTATED    3  2  1  0
  TGFBR2 WILD-TYPE 96 31 98  5
D17V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              3               96
  N1              2               31
  N2              1               98
  N3              0                5
[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, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     4   6
  TGFBR2 WILD-TYPE  80 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      4    6
  TGFBR2 WILD-TYPE   80  216
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              4               80
  MALE                6              216
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0  10
  TGFBR2 WILD-TYPE  81 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0   10
  TGFBR2 WILD-TYPE   81  215
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               0               81
  YES             10              215
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR2 MUTATED                                  0     0
  TGFBR2 WILD-TYPE                                1     5
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED                           3     7
  TGFBR2 WILD-TYPE                        25   258
D17V10, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                5
  BLACK OR AFRICAN AMERICAN                     3               25
  WHITE                                         7              258
[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"
D17V11, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0   9
  TGFBR2 WILD-TYPE  14 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    9
  TGFBR2 WILD-TYPE   14  274
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              9              274
[1] 2 2
[1] FALSE

Clustering(18) Variable = PIK3CA MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    37  19
  PIK3CA WILD-TYPE 131  72
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              56              203 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19               72 
$`PIK3CA MUTATED`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5557 TCGA-BB-4223 TCGA-BB-7863 TCGA-BB-7866 
        1983          248          623         2878          423          638 
TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5373 
         721         1330         1268         1081         1980          683 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6998 
         630          628         1970          224          735           46 
TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CR-5243 TCGA-CR-5249 
        1399         1253         1974         1407         2562         1152 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7374 
        1966         1050          234         1440         1979           30 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5435 
         898          930          181         1077         1472         1438 
TCGA-CV-5442 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        2327         1899         1969         1969         1966         1969 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 
        1960         1099         1974         1948         1957         1947 
TCGA-CX-7082 TCGA-D6-6517 TCGA-D6-6824 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-H7-7774 
         317          292           77         1030          575          407 
TCGA-HD-7754 TCGA-HL-7533 
          25         1057 

$`PIK3CA WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          283          415          276          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          725         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         187          278          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4725 
         536          687         1153          428          436         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1988         1007         1045          173         1980 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5374 
        1681         1977         1966         1966         1975          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          629          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          98          202         1110          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         432          429         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
        1422         1393          317          129         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959         1959         1179         1007          509 
TCGA-CQ-7068 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        1309          358         1663          799         1777         1521 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          354          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        1435         1191         1245         1960          105          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         889          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 
         946          908          216          156          911         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         3295          584          546         1978 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
         641         1970         1948         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1948         1957         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1967         1976         1955         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7085 TCGA-CX-7086 
        1984         1958         1959         1981          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          773          701          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
        1778         1081          516          548         1965          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-HD-7229 
         622          299          368          324         1131            2 
TCGA-HD-7753 TCGA-HD-7917 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
           5           37          485          122          441 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25                2 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2878             3837 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          1125.5            933.0 
[1] "25.0 - 2878.0 (1125.5)" "2.0 - 3837.0 (933.0)"  
[1] "hr=" "1.4"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PIK3CA MUTATED         4        6         7        35         2
  PIK3CA WILD-TYPE      13       40        35       114         4
D18V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                4               13
  STAGE II               6               40
  STAGE III              7               35
  STAGE IVA             35              114
  STAGE IVB              2                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  PIK3CA MUTATED    5 13 13 24
  PIK3CA WILD-TYPE 19 64 50 77
D18V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              5               19
  T2             13               64
  T3             13               50
  T4             24               77
[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"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   24  7 18  2
  PIK3CA WILD-TYPE 75 26 81  3
D18V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             24               75
  N1              7               26
  N2             18               81
  N3              2                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    23  41
  PIK3CA WILD-TYPE  61 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     23   41
  PIK3CA WILD-TYPE   61  181
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             23               61
  MALE               41              181
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    17  47
  PIK3CA WILD-TYPE  64 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     17   47
  PIK3CA WILD-TYPE   64  178
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              17               64
  YES             47              178
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     1
  PIK3CA WILD-TYPE                                1     4
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           1    60
  PIK3CA WILD-TYPE                        27   205
D18V10, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                4
  BLACK OR AFRICAN AMERICAN                     1               27
  WHITE                                        60              205
[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"
D18V11, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     3  60
  PIK3CA WILD-TYPE  11 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3   60
  PIK3CA WILD-TYPE   11  223
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  3               11
  NOT HISPANIC OR LATINO             60              223
[1] 2 2
[1] FALSE

Clustering(19) Variable = FBXW7 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED     8   4
  FBXW7 WILD-TYPE 160  87
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             12             247 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              87 
$`FBXW7 MUTATED`
TCGA-BA-6868 TCGA-BB-4228 TCGA-CN-4730 TCGA-CN-5366 TCGA-CN-6992 TCGA-CQ-5327 
         190          558          817         1966          394         1660 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CR-7379 TCGA-CR-7398 TCGA-CV-6436 TCGA-CV-7095 
         317         1000         1036          156         1899         1970 

$`FBXW7 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636         1747          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         113          236          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        1153          428          436          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
        1230         1151          392          993          642          758 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988         1007         1045          173         1980 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
        1081         1681         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
         202         1110          224          318          611          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         432          429           46         1466         1207          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1422         1393         1399          129         1253         1974 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          216          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 
         215         1315         1665          641         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1947         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 
        1984         1958         1959         1981          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         491          154          568         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 
         299          368          324         1131          407            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
           5           25           37         1057          485          122 
TCGA-IQ-7632 
         441 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
            156               2 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1970            3837 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          908.5           997.0 
[1] "156.0 - 1970.0 (908.5)" "2.0 - 3837.0 (997.0)"  
[1] "hr=" "1.4"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FBXW7 MUTATED         0        3         3         6         1
  FBXW7 WILD-TYPE      17       43        39       143         5
D19V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0              17
  STAGE II              3              43
  STAGE III             3              39
  STAGE IVA             6             143
  STAGE IVB             1               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  FBXW7 MUTATED    0  4  5  5
  FBXW7 WILD-TYPE 24 73 58 96
D19V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             0              24
  T2             4              73
  T3             5              58
  T4             5              96
[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"
                 vv
clus              N0 N1 N2 N3
  FBXW7 MUTATED    3  1  4  1
  FBXW7 WILD-TYPE 96 32 95  4
D19V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             3              96
  N1             1              32
  N2             4              95
  N3             1               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED     6   9
  FBXW7 WILD-TYPE  78 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      6    9
  FBXW7 WILD-TYPE   78  213
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             6              78
  MALE               9             213
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     5  10
  FBXW7 WILD-TYPE  76 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      5   10
  FBXW7 WILD-TYPE   76  215
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              5              76
  YES            10             215
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  0     1
  FBXW7 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           2    11
  FBXW7 WILD-TYPE                        26   254
D19V10, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    2              26
  WHITE                                       11             254
[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"
D19V11, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1  13
  FBXW7 WILD-TYPE  13 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1   13
  FBXW7 WILD-TYPE   13  270
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO            13             270
[1] 2 2
[1] FALSE

Clustering(20) Variable = RB1 MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     9   0
  RB1 WILD-TYPE 159  91
  RB1 MUTATED RB1 WILD-TYPE 
            9           250 
  RB1 MUTATED RB1 WILD-TYPE 
            0            91 
$`RB1 MUTATED`
TCGA-CN-5360 TCGA-CQ-5327 TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7398 
        1081         1660          234          105           30          156 
TCGA-CR-7402 TCGA-CX-7085 TCGA-DQ-7594 
         911          321          368 

$`RB1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
          46         1466         1207          654         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1399          317          129         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          354          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        1435         1191         1440         1245         1960         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759          889          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         181         1077         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        1958         1959         1981          317          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         568         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 
        1965          575          775          622          299          324 
TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
        1131          407            2            5           25           37 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        1057          485          122          441 

  RB1 MUTATED RB1 WILD-TYPE 
           30             2 
  RB1 MUTATED RB1 WILD-TYPE 
         1660          3837 
  RB1 MUTATED RB1 WILD-TYPE 
          321          1007 
[1] "30.0 - 1660.0 (321.0)" "2.0 - 3837.0 (1007.0)"
[1] "hr="     "3400000"
D20V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RB1 MUTATED         2        1         0         3         0
  RB1 WILD-TYPE      15       45        42       146         6
D20V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             2            15
  STAGE II            1            45
  STAGE III           0            42
  STAGE IVA           3           146
  STAGE IVB           0             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  RB1 MUTATED    2  1  1  2
  RB1 WILD-TYPE 22 76 62 99
D20V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           2            22
  T2           1            76
  T3           1            62
  T4           2            99
[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"
               vv
clus            N0 N1 N2 N3
  RB1 MUTATED    4  0  2  0
  RB1 WILD-TYPE 95 33 97  5
D20V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           4            95
  N1           0            33
  N2           2            97
  N3           0             5
[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, binary
               cls
clus              0   1
  RB1 MUTATED     5   5
  RB1 WILD-TYPE  79 217
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5    5
  RB1 WILD-TYPE   79  217
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           5            79
  MALE             5           217
[1] 2 2
[1] FALSE
D20V7, binary
               cls
clus              0   1
  RB1 MUTATED     2   8
  RB1 WILD-TYPE  79 217
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      2    8
  RB1 WILD-TYPE   79  217
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            2            79
  YES           8           217
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     1
  RB1 WILD-TYPE                                1     4
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           0     9
  RB1 WILD-TYPE                        28   256
D20V10, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             4
  BLACK OR AFRICAN AMERICAN                  0            28
  WHITE                                      9           256
[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"
D20V11, binary
               cls
clus              0   1
  RB1 MUTATED     0   9
  RB1 WILD-TYPE  14 274
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    9
  RB1 WILD-TYPE   14  274
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0            14
  NOT HISPANIC OR LATINO           9           274
[1] 2 2
[1] FALSE

Clustering(21) Variable = CTCF MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     6   3
  CTCF WILD-TYPE 162  88
  CTCF MUTATED CTCF WILD-TYPE 
             9            250 
  CTCF MUTATED CTCF WILD-TYPE 
             3             88 
$`CTCF MUTATED`
TCGA-BA-5151 TCGA-CQ-5327 TCGA-CQ-5334 TCGA-CQ-6228 TCGA-CR-7382 TCGA-CV-7102 
         722         1660          129         1959          796         1945 
TCGA-CV-7242 TCGA-H7-7774 TCGA-HL-7533 
        1095          407         1057 

$`CTCF WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         113          236          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 TCGA-CN-4725 
         638         1153          428          436          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
          46         1466         1207          654         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 
        1399          317         1253         1974         1000         1407 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 
        1057          985         1959         1179         1007          509 
TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
        1309         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 
        1970         1970         1936         1959         1939         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1979         1952         1444          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1958         1959         1981          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         154          568         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         368          324         1131            2            5           25 
TCGA-HD-7917 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          37          485          122          441 

  CTCF MUTATED CTCF WILD-TYPE 
           129              2 
  CTCF MUTATED CTCF WILD-TYPE 
          1959           3837 
  CTCF MUTATED CTCF WILD-TYPE 
          1057            995 
[1] "129.0 - 1959.0 (1057.0)" "2.0 - 3837.0 (995.0)"   
[1] "hr=" "1.9"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CTCF MUTATED         0        2         0         8         0
  CTCF WILD-TYPE      17       44        42       141         6
D21V3, multiclass
           clus
vv          CTCF MUTATED CTCF WILD-TYPE
  STAGE I              0             17
  STAGE II             2             44
  STAGE III            0             42
  STAGE IVA            8            141
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  CTCF MUTATED    1  3  3  3
  CTCF WILD-TYPE 23 74 60 98
D21V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            1             23
  T2            3             74
  T3            3             60
  T4            3             98
[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"
                vv
clus             N0 N1 N2 N3
  CTCF MUTATED    4  0  5  0
  CTCF WILD-TYPE 95 33 94  5
D21V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            4             95
  N1            0             33
  N2            5             94
  N3            0              5
[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, binary
                cls
clus               0   1
  CTCF MUTATED     5   6
  CTCF WILD-TYPE  79 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      5    6
  CTCF WILD-TYPE   79  216
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE            5             79
  MALE              6            216
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  CTCF MUTATED     4   7
  CTCF WILD-TYPE  77 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      4    7
  CTCF WILD-TYPE   77  218
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO             4             77
  YES            7            218
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  0     1
  CTCF WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED                           1     9
  CTCF WILD-TYPE                        27   256
D21V10, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              4
  BLACK OR AFRICAN AMERICAN                   1             27
  WHITE                                       9            256
[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"
D21V11, binary
                cls
clus               0   1
  CTCF MUTATED     0  11
  CTCF WILD-TYPE  14 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   11
  CTCF WILD-TYPE   14  272
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO           11            272
[1] 2 2
[1] FALSE

Clustering(22) Variable = KDM6A MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     5   1
  KDM6A WILD-TYPE 163  90
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             253 
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              90 
$`KDM6A MUTATED`
TCGA-CN-5355 TCGA-CR-7368 TCGA-CV-5441 TCGA-CV-6935 TCGA-HD-7229 TCGA-HD-7753 
        1007         1245         2886         1969            2            5 

$`KDM6A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
          46         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
         479         1956         1435         1191         1440         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
        1438          584          546         1978         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 
         701           77          491          154          568         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1081          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-H7-7774 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
         407           25           37         1057          485          122 
TCGA-IQ-7632 
         441 

  KDM6A MUTATED KDM6A WILD-TYPE 
              2              25 
  KDM6A MUTATED KDM6A WILD-TYPE 
           2886            3837 
  KDM6A MUTATED KDM6A WILD-TYPE 
           1126             993 
[1] "2.0 - 2886.0 (1126.0)" "25.0 - 3837.0 (993.0)"
[1] "hr=" "3.3"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KDM6A MUTATED         1        1         0         6         0
  KDM6A WILD-TYPE      16       45        42       143         6
D22V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               1              16
  STAGE II              1              45
  STAGE III             0              42
  STAGE IVA             6             143
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  KDM6A MUTATED    1  1  1  5
  KDM6A WILD-TYPE 23 76 62 96
D22V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             1              23
  T2             1              76
  T3             1              62
  T4             5              96
[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"
                 vv
clus              N0 N1 N2 N3
  KDM6A MUTATED    4  1  2  0
  KDM6A WILD-TYPE 95 32 97  5
D22V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0             4              95
  N1             1              32
  N2             2              97
  N3             0               5
[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, binary
                 cls
clus                0   1
  KDM6A MUTATED     1   7
  KDM6A WILD-TYPE  83 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    7
  KDM6A WILD-TYPE   83  215
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             1              83
  MALE               7             215
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     1   7
  KDM6A WILD-TYPE  80 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    7
  KDM6A WILD-TYPE   80  218
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              1              80
  YES             7             218
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     0
  KDM6A WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3     5
  KDM6A WILD-TYPE                        25   260
D22V10, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               5
  BLACK OR AFRICAN AMERICAN                    3              25
  WHITE                                        5             260
[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"
D22V11, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   8
  KDM6A WILD-TYPE  14 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    8
  KDM6A WILD-TYPE   14  275
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             8             275
[1] 2 2
[1] FALSE

Clustering(23) Variable = ELF4 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  ELF4 MUTATED     3   2
  ELF4 WILD-TYPE 165  89
  ELF4 MUTATED ELF4 WILD-TYPE 
             5            254 
  ELF4 MUTATED ELF4 WILD-TYPE 
             2             89 
$`ELF4 MUTATED`
TCGA-CQ-5324 TCGA-CR-5248 TCGA-CR-7376 TCGA-CV-7099 TCGA-CV-7406 
        1207         1663          972         1936         1974 

$`ELF4 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
        1045          173         1980         1081         1681         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         429           46         1466          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 
         105         1979          759          889           30         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
        3837         1959         1970         1970         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 
        1948         1955         1957         1947         1937         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 
        1937         1984         1958         1959         1981          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         321          237          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 
          77          491          154          568         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 
         622          299          368          324         1131          407 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 
           2            5           25           37         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 
         122          441 

  ELF4 MUTATED ELF4 WILD-TYPE 
           972              2 
  ELF4 MUTATED ELF4 WILD-TYPE 
          1974           3837 
  ELF4 MUTATED ELF4 WILD-TYPE 
          1663            989 
[1] "972.0 - 1974.0 (1663.0)" "2.0 - 3837.0 (989.0)"   
[1] "hr=" "1.1"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ELF4 MUTATED         0        2         2         0         0
  ELF4 WILD-TYPE      17       44        40       149         6
D23V3, multiclass
           clus
vv          ELF4 MUTATED ELF4 WILD-TYPE
  STAGE I              0             17
  STAGE II             2             44
  STAGE III            2             40
  STAGE IVA            0            149
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELF4 MUTATED     0   3   1   0
  ELF4 WILD-TYPE  24  74  62 101
D23V4, multiclass
    clus
vv   ELF4 MUTATED ELF4 WILD-TYPE
  T1            0             24
  T2            3             74
  T3            1             62
  T4            0            101
[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"
                vv
clus             N0 N1 N2 N3
  ELF4 MUTATED    2  1  0  0
  ELF4 WILD-TYPE 97 32 99  5
D23V5, multiclass
    clus
vv   ELF4 MUTATED ELF4 WILD-TYPE
  N0            2             97
  N1            1             32
  N2            0             99
  N3            0              5
[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, binary
                cls
clus               0   1
  ELF4 MUTATED     1   4
  ELF4 WILD-TYPE  83 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      1    4
  ELF4 WILD-TYPE   83  218
        clus
vv       ELF4 MUTATED ELF4 WILD-TYPE
  FEMALE            1             83
  MALE              4            218
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  ELF4 MUTATED     0   5
  ELF4 WILD-TYPE  81 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      0    5
  ELF4 WILD-TYPE   81  220
     clus
vv    ELF4 MUTATED ELF4 WILD-TYPE
  NO             0             81
  YES            5            220
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELF4 MUTATED                                  0     0
  ELF4 WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ELF4 MUTATED                           0     5
  ELF4 WILD-TYPE                        28   260
D23V10, multiclass
                                  clus
vv                                 ELF4 MUTATED ELF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              5
  BLACK OR AFRICAN AMERICAN                   0             28
  WHITE                                       5            260
[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"
D23V11, binary
                cls
clus               0   1
  ELF4 MUTATED     0   4
  ELF4 WILD-TYPE  14 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      0    4
  ELF4 WILD-TYPE   14  279
                        clus
vv                       ELF4 MUTATED ELF4 WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            4            279
[1] 2 2
[1] FALSE

Clustering(24) Variable = RHOA MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     1   3
  RHOA WILD-TYPE 167  88
  RHOA MUTATED RHOA WILD-TYPE 
             4            255 
  RHOA MUTATED RHOA WILD-TYPE 
             3             88 
$`RHOA MUTATED`
TCGA-CN-6998 TCGA-CV-7102 TCGA-CV-7410 TCGA-DQ-5625 
          46         1945         1948         1081 

$`RHOA WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
        1045          173         1980         1081         1681         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         429         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         1974         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1981          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
         407            2            5           25           37         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         485          122          441 

  RHOA MUTATED RHOA WILD-TYPE 
            46              2 
  RHOA MUTATED RHOA WILD-TYPE 
          1948           3837 
  RHOA MUTATED RHOA WILD-TYPE 
          1513            993 
[1] "46.0 - 1948.0 (1513.0)" "2.0 - 3837.0 (993.0)"  
[1] "hr=" "4.5"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RHOA MUTATED         0        0         1         2         0
  RHOA WILD-TYPE      17       46        41       147         6
D24V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              0             17
  STAGE II             0             46
  STAGE III            1             41
  STAGE IVA            2            147
  STAGE IVB            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOA MUTATED     0   1   2   0
  RHOA WILD-TYPE  24  76  61 101
D24V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0             24
  T2            1             76
  T3            2             61
  T4            0            101
[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"
                vv
clus             N0 N1 N2 N3
  RHOA MUTATED    0  1  2  0
  RHOA WILD-TYPE 99 32 97  5
D24V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            0             99
  N1            1             32
  N2            2             97
  N3            0              5
[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, binary
                cls
clus               0   1
  RHOA MUTATED     2   2
  RHOA WILD-TYPE  82 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      2    2
  RHOA WILD-TYPE   82  220
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            2             82
  MALE              2            220
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus               0   1
  RHOA MUTATED     0   4
  RHOA WILD-TYPE  81 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0    4
  RHOA WILD-TYPE   81  221
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             0             81
  YES            4            221
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHOA MUTATED                                  0     0
  RHOA WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED                           0     4
  RHOA WILD-TYPE                        28   261
D24V10, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              5
  BLACK OR AFRICAN AMERICAN                   0             28
  WHITE                                       4            261
[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"
D24V11, binary
                cls
clus               0   1
  RHOA MUTATED     0   4
  RHOA WILD-TYPE  14 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0    4
  RHOA WILD-TYPE   14  279
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            4            279
[1] 2 2
[1] FALSE

Clustering(25) Variable = HLA-B MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     6   1
  HLA-B WILD-TYPE 162  90
  HLA-B MUTATED HLA-B WILD-TYPE 
              7             252 
  HLA-B MUTATED HLA-B WILD-TYPE 
              1              90 
$`HLA-B MUTATED`
TCGA-CN-4723 TCGA-CQ-5324 TCGA-CR-6481 TCGA-CR-7395 TCGA-CV-5973 TCGA-CV-7099 
         721         1207          311          930         2641         1936 
TCGA-D6-6516 
         773 

$`HLA-B WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4725 
         687          638         1153          428          436         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         642          758         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 
         173         1980         1081         1681         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
          46         1466          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 
        1399          317          129         1253         1974         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1407         1057          985         1959         1959         1179 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1007          509         1309         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 
        1125         1971          514         1969          362          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         519          406          701         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1947         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 
        1984         1958         1959         1981          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          828          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         154          568         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 
         368          324         1131          407            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          25           37         1057          485          122          441 

  HLA-B MUTATED HLA-B WILD-TYPE 
            311               2 
  HLA-B MUTATED HLA-B WILD-TYPE 
           2641            3837 
  HLA-B MUTATED HLA-B WILD-TYPE 
          930.0           998.5 
[1] "311.0 - 2641.0 (930.0)" "2.0 - 3837.0 (998.5)"  
[1] "hr=" "2.9"
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HLA-B MUTATED         1        2         2         2         0
  HLA-B WILD-TYPE      16       44        40       147         6
D25V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               1              16
  STAGE II              2              44
  STAGE III             2              40
  STAGE IVA             2             147
  STAGE IVB             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  HLA-B MUTATED    1  2  2  2
  HLA-B WILD-TYPE 23 75 61 99
D25V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             1              23
  T2             2              75
  T3             2              61
  T4             2              99
[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"
                 vv
clus              N0 N1 N2 N3
  HLA-B MUTATED    5  1  0  0
  HLA-B WILD-TYPE 94 32 99  5
D25V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             5              94
  N1             1              32
  N2             0              99
  N3             0               5
[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, binary
                 cls
clus                0   1
  HLA-B MUTATED     4   4
  HLA-B WILD-TYPE  80 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    4
  HLA-B WILD-TYPE   80  218
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             4              80
  MALE               4             218
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     0   8
  HLA-B WILD-TYPE  81 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0    8
  HLA-B WILD-TYPE   81  217
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              0              81
  YES             8             217
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-B MUTATED                                  0     0
  HLA-B WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED                           0     8
  HLA-B WILD-TYPE                        28   257
D25V10, multiclass
                                  clus
vv                                 HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               5
  BLACK OR AFRICAN AMERICAN                    0              28
  WHITE                                        8             257
[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"
D25V11, binary
                 cls
clus                0   1
  HLA-B MUTATED     0   7
  HLA-B WILD-TYPE  14 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0    7
  HLA-B WILD-TYPE   14  276
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             7             276
[1] 2 2
[1] FALSE

Clustering(26) Variable = PRSS1 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  PRSS1 MUTATED     3   1
  PRSS1 WILD-TYPE 165  90
  PRSS1 MUTATED PRSS1 WILD-TYPE 
              4             255 
  PRSS1 MUTATED PRSS1 WILD-TYPE 
              1              90 
$`PRSS1 MUTATED`
TCGA-CQ-5329 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7370 
        1422         1969          354          105 

$`PRSS1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         384          113          236          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4723 
         687          638         1153          428          436          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
        1045          173         1980         1081         1681         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         429           46         1466         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1393         1399          317          129         1253         1974 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1407         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
        1179         1007          509         1309         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125         1971          514          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        1435         1191         1440         1245         1960         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         215         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 
         701           77          491          154          568         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1081          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
         775          622          299          368          324         1131 
TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
         407            2            5           25           37         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         485          122          441 

  PRSS1 MUTATED PRSS1 WILD-TYPE 
            105               2 
  PRSS1 MUTATED PRSS1 WILD-TYPE 
           1969            3837 
  PRSS1 MUTATED PRSS1 WILD-TYPE 
            888             997 
[1] "105.0 - 1969.0 (888.0)" "2.0 - 3837.0 (997.0)"  
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PRSS1 MUTATED         0        1         1         2         1
  PRSS1 WILD-TYPE      17       45        41       147         5
D26V3, multiclass
           clus
vv          PRSS1 MUTATED PRSS1 WILD-TYPE
  STAGE I               0              17
  STAGE II              1              45
  STAGE III             1              41
  STAGE IVA             2             147
  STAGE IVB             1               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  PRSS1 MUTATED    0  1  1  3
  PRSS1 WILD-TYPE 24 76 62 98
D26V4, multiclass
    clus
vv   PRSS1 MUTATED PRSS1 WILD-TYPE
  T1             0              24
  T2             1              76
  T3             1              62
  T4             3              98
[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"
                 vv
clus              N0 N1 N2 N3
  PRSS1 MUTATED    1  0  2  1
  PRSS1 WILD-TYPE 98 33 97  4
D26V5, multiclass
    clus
vv   PRSS1 MUTATED PRSS1 WILD-TYPE
  N0             1              98
  N1             0              33
  N2             2              97
  N3             1               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                 cls
clus                0   1
  PRSS1 MUTATED     6   1
  PRSS1 WILD-TYPE  78 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS1 MUTATED      6    1
  PRSS1 WILD-TYPE   78  221
        clus
vv       PRSS1 MUTATED PRSS1 WILD-TYPE
  FEMALE             6              78
  MALE               1             221
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  PRSS1 MUTATED     0   7
  PRSS1 WILD-TYPE  81 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS1 MUTATED      0    7
  PRSS1 WILD-TYPE   81  218
     clus
vv    PRSS1 MUTATED PRSS1 WILD-TYPE
  NO              0              81
  YES             7             218
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "PRSS1 MUTATED"         
clus
  PRSS1 MUTATED PRSS1 WILD-TYPE 
              1             167 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5555 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-BA-5556      TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-BA-6871      TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-BB-4217      TCGA-BB-4225      TCGA-BB-4227      TCGA-BB-4228 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-BB-7862      TCGA-BB-7864      TCGA-BB-7870      TCGA-BB-7871 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-4726      TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4729 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-4730      TCGA-CN-4731      TCGA-CN-4735      TCGA-CN-4736 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4740      TCGA-CN-4741 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-4742      TCGA-CN-5355      TCGA-CN-5358      TCGA-CN-5359 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-5360      TCGA-CN-5361      TCGA-CN-5363      TCGA-CN-5365 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-5366      TCGA-CN-5367      TCGA-CN-5373      TCGA-CN-5374 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012      TCGA-CN-6016 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-6017      TCGA-CN-6019      TCGA-CN-6021      TCGA-CN-6023 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-6024      TCGA-CN-6988      TCGA-CN-6989      TCGA-CN-6992 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CN-6994      TCGA-CN-6997      TCGA-CN-6998      TCGA-CQ-5323 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5326      TCGA-CQ-5330 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CQ-5331      TCGA-CQ-5332      TCGA-CQ-6218      TCGA-CQ-6219 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CQ-6221      TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CQ-6227      TCGA-CQ-6228      TCGA-CR-5247      TCGA-CR-5250 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-6467      TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-6482      TCGA-CR-6487      TCGA-CR-6491      TCGA-CR-6492 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7367      TCGA-CR-7368 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-7369      TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7379      TCGA-CR-7383 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-7385      TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-7390      TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CR-7398      TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6936      TCGA-CV-6941 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-7095      TCGA-CV-7097 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7261      TCGA-CV-7263 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-7406      TCGA-CV-7410      TCGA-CV-7418      TCGA-CV-7422 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-7424      TCGA-CV-7427      TCGA-CV-7430      TCGA-CV-7432 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7440      TCGA-CX-7082 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-CX-7085      TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-D6-6517      TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-D6-6827      TCGA-DQ-5625      TCGA-DQ-5629      TCGA-DQ-5630 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589      TCGA-DQ-7590 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7595      TCGA-F7-7848 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-H7-7774      TCGA-HD-7753      TCGA-HD-7754      TCGA-HD-7832 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
     TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632 
"PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" "PRSS1 WILD-TYPE" 
D26V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRSS1 MUTATED                                  0     1
  PRSS1 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRSS1 MUTATED                           1     5
  PRSS1 WILD-TYPE                        27   260
D26V10, multiclass
                                  clus
vv                                 PRSS1 MUTATED PRSS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    1              27
  WHITE                                        5             260
[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"
D26V11, binary
                 cls
clus                0   1
  PRSS1 MUTATED     0   7
  PRSS1 WILD-TYPE  14 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS1 MUTATED      0    7
  PRSS1 WILD-TYPE   14  276
                        clus
vv                       PRSS1 MUTATED PRSS1 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             7             276
[1] 2 2
[1] FALSE

Clustering(27) Variable = GUCY2F MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  GUCY2F MUTATED     4   3
  GUCY2F WILD-TYPE 164  88
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               7              252 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               3               88 
$`GUCY2F MUTATED`
TCGA-BA-5149 TCGA-BA-5152 TCGA-BB-7862 TCGA-BB-7872 TCGA-CN-4740 TCGA-CR-7404 
         248         1288          536          436          811         1472 
TCGA-DQ-7588 
        1965 

$`GUCY2F WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         462          283          415         1983          276          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         236          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7871 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         428          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
         392          817          993          642          758         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          625         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
        1007         1045          173         1980         1081         1681 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1110          224          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         432          429           46         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
        1660         1422         1393         1399          317          129 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
        1253         1974         1000         1407         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1007          509         1309 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
         156          181         1077          911         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1947         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 
        1984         1958         1959         1981          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         491          154          568         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7753 
         368          324         1131          407            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          25           37         1057          485          122          441 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
             248                2 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
            1965             3837 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
           811.0            998.5 
[1] "248.0 - 1965.0 (811.0)" "2.0 - 3837.0 (998.5)"  
[1] "hr=" "2.2"
D27V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  GUCY2F MUTATED         1        0         0         5         0
  GUCY2F WILD-TYPE      16       46        42       144         6
D27V3, multiclass
           clus
vv          GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE I                1               16
  STAGE II               0               46
  STAGE III              0               42
  STAGE IVA              5              144
  STAGE IVB              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  GUCY2F MUTATED    1  0  2  3
  GUCY2F WILD-TYPE 23 77 61 98
D27V4, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  T1              1               23
  T2              0               77
  T3              2               61
  T4              3               98
[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"
                  vv
clus               N0 N1 N2 N3
  GUCY2F MUTATED    4  0  2  0
  GUCY2F WILD-TYPE 95 33 97  5
D27V5, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  N0              4               95
  N1              0               33
  N2              2               97
  N3              0                5
[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, binary
                  cls
clus                 0   1
  GUCY2F MUTATED     2   6
  GUCY2F WILD-TYPE  82 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      2    6
  GUCY2F WILD-TYPE   82  216
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  FEMALE              2               82
  MALE                6              216
[1] 2 2
[1] FALSE
D27V7, binary
                  cls
clus                 0   1
  GUCY2F MUTATED     3   5
  GUCY2F WILD-TYPE  78 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      3    5
  GUCY2F WILD-TYPE   78  220
     clus
vv    GUCY2F MUTATED GUCY2F WILD-TYPE
  NO               3               78
  YES              5              220
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUCY2F MUTATED                                  0     1
  GUCY2F WILD-TYPE                                1     4
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GUCY2F MUTATED                           1     6
  GUCY2F WILD-TYPE                        27   259
D27V10, multiclass
                                  clus
vv                                 GUCY2F MUTATED GUCY2F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                4
  BLACK OR AFRICAN AMERICAN                     1               27
  WHITE                                         6              259
[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"
D27V11, binary
                  cls
clus                 0   1
  GUCY2F MUTATED     0   7
  GUCY2F WILD-TYPE  14 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      0    7
  GUCY2F WILD-TYPE   14  276
                        clus
vv                       GUCY2F MUTATED GUCY2F WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              7              276
[1] 2 2
[1] FALSE
