[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"            "-oTCOADREAD-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/COADREAD-TP/10005910/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/10686949/transformed.cor.cli.txt"

nPatients in clinical file=612, in cluster file=223, common to both=223
[1]  46 223
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          163            60 
  APC MUTATED APC WILD-TYPE 
          163            60 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           117            106 
  TP53 MUTATED TP53 WILD-TYPE 
           117            106 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            97            126 
  KRAS MUTATED KRAS WILD-TYPE 
            97            126 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            20            203 
  NRAS MUTATED NRAS WILD-TYPE 
            20            203 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             197 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             197 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             185 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             185 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             208 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             208 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               24               199 
  FAM123B MUTATED FAM123B WILD-TYPE 
               24               199 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              190 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              190 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              205 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              205 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              20              203 
  ARID1A MUTATED ARID1A WILD-TYPE 
              20              203 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            21            202 
  BRAF MUTATED BRAF WILD-TYPE 
            21            202 
[1] "MGC42105 MUTATION ANALYSIS"
[1] 3
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                11                212 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                11                212 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              14              209 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              14              209 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             13             210 
  CDC27 MUTATED CDC27 WILD-TYPE 
             13             210 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                208 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                208 
[1] "PCDHGB1 MUTATION ANALYSIS"
[1] 3
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                8               215 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                8               215 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             218 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             218 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            10            213 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            10            213 
[1] "PCDHA3 MUTATION ANALYSIS"
[1] 3
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
              12              211 
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
              12              211 
[1] "PCDHA2 MUTATION ANALYSIS"
[1] 3
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
              12              211 
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
              12              211 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             8            215 
  ELF3 MUTATED ELF3 WILD-TYPE 
             8            215 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              4             219 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              4             219 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             213 
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             213 
[1] "CACNG3 MUTATION ANALYSIS"
[1] 3
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              215 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              215 
[1] "PCDHGA7 MUTATION ANALYSIS"
[1] 3
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               218 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               218 
[1] "CCBP2 MUTATION ANALYSIS"
[1] 3
  CCBP2 MUTATED CCBP2 WILD-TYPE 
             10             213 
  CCBP2 MUTATED CCBP2 WILD-TYPE 
             10             213 
[1] "MAP2K4 MUTATION ANALYSIS"
[1] 3
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              11              212 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              11              212 
[1] "PCDHGA9 MUTATION ANALYSIS"
[1] 3
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                6               217 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                6               217 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              8             215 
  RBM10 MUTATED RBM10 WILD-TYPE 
              8             215 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            216 
  PTEN MUTATED PTEN WILD-TYPE 
             7            216 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             17             206 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             17             206 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
             9            214 
  BCOR MUTATED BCOR WILD-TYPE 
             9            214 
[1] "PCDHGB5 MUTATION ANALYSIS"
[1] 3
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
                7               216 
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
                7               216 
[1] "ZFP3 MUTATION ANALYSIS"
[1] 3
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             8            215 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             8            215 
[1] "RWDD2B MUTATION ANALYSIS"
[1] 3
  RWDD2B MUTATED RWDD2B WILD-TYPE 
               7              216 
  RWDD2B MUTATED RWDD2B WILD-TYPE 
               7              216 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                220 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                220 
[1] "ERCC6L MUTATION ANALYSIS"
[1] 3
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               5              218 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               5              218 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             209 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             209 
[1] "KLK2 MUTATION ANALYSIS"
[1] 3
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            220 
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            220 
[1] "TAPBP MUTATION ANALYSIS"
[1] 3
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             218 
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             218 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             214 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             214 
[1] "MORC2 MUTATION ANALYSIS"
[1] 3
  MORC2 MUTATED MORC2 WILD-TYPE 
              5             218 
  MORC2 MUTATED MORC2 WILD-TYPE 
              5             218 
[1] "ABCA8 MUTATION ANALYSIS"
[1] 3
  ABCA8 MUTATED ABCA8 WILD-TYPE 
             12             211 
  ABCA8 MUTATED ABCA8 WILD-TYPE 
             12             211 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             13             210 
  SETD2 MUTATED SETD2 WILD-TYPE 
             13             210 
[1] "ESR1 MUTATION ANALYSIS"
[1] 3
  ESR1 MUTATED ESR1 WILD-TYPE 
            11            212 
  ESR1 MUTATED ESR1 WILD-TYPE 
            11            212 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 223 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
        1419         1331          711          541         1286          472 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1054         1014         1111           31           NA         1186 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 
          31          276          731           NA         1127         1096 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
         245          580           NA           NA          580         1035 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
         882          882          791          395           30          426 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        1034          639           NA          730          546          911 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
         700          638          608          424          608         1643 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
          NA          426           28         1522         1430          457 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
          NA          182           NA         1127          578           NA 
TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
          NA           NA           NA          821           30           30 
TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        1066           NA           NA          761           31          547 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
         485         1186         1126          454           NA          518 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
          30           NA         1006           NA         1096          975 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
          30          945          945         1612          518          731 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA          912           NA          549          943           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
         395          730         1004          791           NA          638 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        1035           61          489         1551          397         1036 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 
         791          761          730          822          822           NA 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
         580           NA          822          424         1157          578 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
         913         1035          549          549          518           NA 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
         822         1278           30          518          456          669 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1064          457           30          974          365          943 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
         943           NA           31         1065           31         1005 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 
        1065          791         1126           NA           NA         1581 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        1216           NA           NA           28         1247         1216 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 
          NA         1246           NA           NA          546         1309 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
         412          387           NA           NA          365          974 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
         244          215           31           61           NA           31 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1400         1035           NA         1522          366          184 
TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
          NA           NA           30          485          608           NA 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
         608          243           30           30           NA          608 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
          31         1124          518          396         1065          426 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
          31         1461           NA          974          608          853 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-A002 
        1096          427           31          518           NA          638 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
         424          183          790          700         1126          485 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1096          276          365         2130         1947          334 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1520           NA           NA         1885         1247         1157 
TCGA-AG-A036 
        3562 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=98,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PRIMARY.SITE.OF.DISEASE"  
 [3] "NEOPLASM.DISEASESTAGE"     "PATHOLOGY.T.STAGE"        
 [5] "PATHOLOGY.N.STAGE"         "PATHOLOGY.M.STAGE"        
 [7] "GENDER"                    "HISTOLOGICAL.TYPE"        
 [9] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 223 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=49, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  47 149  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  47 149  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  47 149  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  47 149  18 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
133  44  46 
[1] "table(vv)"
vv
 N0  N1  N2 
133  44  46 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
133  44  46 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
133  44  46 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=18, binary=FALSE, numeric=TRUE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2             0   1
  APC MUTATED   125  23
  APC WILD-TYPE  44  12
  APC MUTATED APC WILD-TYPE 
          148            56 
  APC MUTATED APC WILD-TYPE 
           23            12 
$`APC MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3519 
       43.76        17.79        34.65        33.34        36.53         9.07 
TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       37.05        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       29.95        23.01        20.98        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
       37.05        19.00        36.00        26.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
        0.99        38.99        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 
       29.98         2.01        12.99        24.00        33.01         2.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       27.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        41.00        18.05 
TCGA-AY-4071 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3580 
        0.95        43.04        13.55        12.72        10.39         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
        2.01        50.04        12.03         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 
       20.98        13.94         6.02        25.97        37.02        36.03 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

$`APC WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-AA-3514 TCGA-AA-3516 
       46.65        23.38        42.28        15.52         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3696 
       29.00         0.99        19.99        54.02         0.92         5.03 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3949 
       14.93        24.03        27.02        18.05        31.00        26.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F 
       20.98         2.01        19.07        13.94        30.02        34.03 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A02Y 
       42.02         0.99         0.99        12.00        38.07        39.98 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       40.96        16.31        17.95        36.03        12.00        32.02 
TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A014 
        1.02         6.05        15.95        17.03        23.01        15.95 
TCGA-AG-A016 TCGA-AG-A01L 
        9.07        12.00 

  APC MUTATED APC WILD-TYPE 
         0.92          0.92 
  APC MUTATED APC WILD-TYPE 
       117.11         54.02 
  APC MUTATED APC WILD-TYPE 
       22.500        18.015 
[1] "0.9 - 117.1 (22.5)" "0.9 - 54.0 (18.0)" 
[1] "hr=" "1.5"
D1V2, continuous
D1V3, binary
               cls
clus              0   1
  APC MUTATED   106  55
  APC WILD-TYPE  47  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    106   55
  APC WILD-TYPE   47   13
        clus
vv       APC MUTATED APC WILD-TYPE
  COLON          106            47
  RECTUM          55            13
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  APC MUTATED        38       14        42         3        14          1
  APC WILD-TYPE      11        6        15         1         4          1
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED           12         13       24         1
  APC WILD-TYPE          8          7        7         0
D1V4, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             38            11
  STAGE II            14             6
  STAGE IIA           42            15
  STAGE IIB            3             1
  STAGE III           14             4
  STAGE IIIA           1             1
  STAGE IIIB          12             8
  STAGE IIIC          13             7
  STAGE IV            24             7
  STAGE IVA            1             0
[1] 10  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
  APC MUTATED     7  36 107  13
  APC WILD-TYPE   2  11  42   5
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           7             2
  T2          36            11
  T3         107            42
  T4          13             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"
               vv
clus            N0 N1 N2
  APC MUTATED   99 32 32
  APC WILD-TYPE 34 12 14
D1V6, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          99            34
  N1          32            12
  N2          32            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A
  APC MUTATED   136  24   1
  APC WILD-TYPE  53   7   0
D1V7, multiclass
     clus
vv    APC MUTATED APC WILD-TYPE
  M0          136            53
  M1           24             7
  M1A           1             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
               cls
clus             0  1
  APC MUTATED   71 92
  APC WILD-TYPE 36 24
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     71   92
  APC WILD-TYPE   36   24
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          71            36
  MALE            92            24
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APC MUTATED                     91                            14
  APC WILD-TYPE                   39                             8
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APC MUTATED                      46                              6
  APC WILD-TYPE                    11                              2
D1V9, multiclass
                                clus
vv                               APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                    91            39
  COLON MUCINOUS ADENOCARCINOMA           14             8
  RECTAL ADENOCARCINOMA                   46            11
  RECTAL MUCINOUS ADENOCARCINOMA           6             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  APC MUTATED   135   1  22   1
  APC WILD-TYPE  52   1   5   0
D1V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0         135            52
  R1           1             1
  R2          22             5
  RX           1             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"
D1V11, continuous

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   94 17
  TP53 WILD-TYPE 75 18
  TP53 MUTATED TP53 WILD-TYPE 
           111             93 
  TP53 MUTATED TP53 WILD-TYPE 
            17             18 
$`TP53 MUTATED`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       43.76        23.38        42.28        15.52        34.65        36.53 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3531 
       38.99         9.07        24.03        36.03        19.07        34.03 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       12.99        21.01        13.02        24.00        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3681 
       19.99        13.94         2.01        14.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 
       37.05         0.99        37.02        14.93         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L 
       27.02        13.94        19.00        30.02        34.03        17.03 
TCGA-AA-A00O TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       27.02        14.99        34.98         0.99        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H 
       31.00         1.02        33.04        37.02        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
        5.03        41.00        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       43.04        12.72        10.39        12.00        32.02         7.07 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       46.03         2.01        50.04         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.99         7.99        19.99        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        1.02        17.03         6.02        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N 
        9.07        70.03        64.01        10.98         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

$`TP53 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-3808 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       46.65        17.79        33.34         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       37.05         8.05        19.07        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3562 
        0.99        14.01        33.99        17.95        29.95        19.99 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3688 
       54.02         0.92        50.04        47.01        11.01        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3846 
       25.02         1.02        17.98        15.95        38.99        17.03 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3939 
       36.03        32.05        53.00        29.98        31.00        12.99 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3986 
       33.01         2.01         2.01        16.08        13.05        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
        7.96        27.02        38.04        18.05        18.05         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01I 
       42.02         0.99        17.03        21.99        15.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       38.07         1.02        35.01        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AF-2692 TCGA-AG-3574 
       51.98         0.92        39.98        18.05        13.55        36.03 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        8.02         1.02         2.01        24.00         1.02        34.03 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       12.03         6.05         0.99         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A015 
       13.02        14.01        20.98        13.94        25.97        36.03 
TCGA-AG-A01L TCGA-AG-A025 TCGA-AG-A02G 
       12.00        49.97        38.96 

  TP53 MUTATED TP53 WILD-TYPE 
          0.95           0.92 
  TP53 MUTATED TP53 WILD-TYPE 
        117.11          54.02 
  TP53 MUTATED TP53 WILD-TYPE 
         23.01          19.00 
[1] "0.9 - 117.1 (23.0)" "0.9 - 54.0 (19.0)" 
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  TP53 MUTATED   72 44
  TP53 WILD-TYPE 81 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     72   44
  TP53 WILD-TYPE   81   24
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  COLON            72             81
  RECTUM           44             24
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TP53 MUTATED        25        9        26         2         8          2
  TP53 WILD-TYPE      24       11        31         2        10          0
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED           12         14       17         1
  TP53 WILD-TYPE          8          6       14         0
D2V4, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              25             24
  STAGE II              9             11
  STAGE IIA            26             31
  STAGE IIB             2              2
  STAGE III             8             10
  STAGE IIIA            2              0
  STAGE IIIB           12              8
  STAGE IIIC           14              6
  STAGE IV             17             14
  STAGE IVA             1              0
[1] 10  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    4 25 79  9
  TP53 WILD-TYPE  5 22 70  9
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            4              5
  T2           25             22
  T3           79             70
  T4            9              9
[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
  TP53 MUTATED   65 25 27
  TP53 WILD-TYPE 68 19 19
D2V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           65             68
  N1           25             19
  N2           27             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             M0 M1 M1A
  TP53 MUTATED   97 17   1
  TP53 WILD-TYPE 92 14   0
D2V7, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  M0            97             92
  M1            17             14
  M1A            1              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED   53 64
  TP53 WILD-TYPE 54 52
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     53   64
  TP53 WILD-TYPE   54   52
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           53             54
  MALE             64             52
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TP53 MUTATED                     67                             4
  TP53 WILD-TYPE                   63                            18
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TP53 MUTATED                      40                              4
  TP53 WILD-TYPE                    17                              4
D2V9, multiclass
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                     67             63
  COLON MUCINOUS ADENOCARCINOMA             4             18
  RECTAL ADENOCARCINOMA                    40             17
  RECTAL MUCINOUS ADENOCARCINOMA            4              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"
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   98  2 14  0
  TP53 WILD-TYPE 89  0 13  1
D2V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           98             89
  R1            2              0
  R2           14             13
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous

Clustering(3) Variable = KRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   76 12
  KRAS WILD-TYPE 93 23
  KRAS MUTATED KRAS WILD-TYPE 
            88            116 
  KRAS MUTATED KRAS WILD-TYPE 
            12             23 
$`KRAS MUTATED`
TCGA-A6-2683 TCGA-A6-3808 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3532 
       15.52        33.34        24.03        37.05        19.07        29.00 
TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       33.99        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3715 
        0.92        50.04        11.01         5.98         5.03         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 
        0.99        38.99        37.02        14.93         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       36.03        53.00        29.98         2.01        12.99        24.00 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        25.02        24.00        19.07        27.02        38.04 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G 
       18.05         4.01        42.02        14.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       31.00        31.00        35.01        26.01        37.02        51.98 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AF-2689 
        0.92        41.00        39.98        18.05        40.96        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       43.04        13.55        12.00         8.02         7.07         2.01 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        1.02         2.01        50.04        12.03         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-3902 
        0.99         0.99        36.95        13.02         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        28.04        14.04        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01W TCGA-AG-A020 
       25.97        23.01        15.95        36.03        70.03        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97        61.97        41.00        38.04 

$`KRAS WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-3807 
       46.65        43.76        23.38        17.79        42.28        34.65 
TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       36.53         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       36.03         8.05        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       17.95        19.99        54.02         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3811 
       15.02        37.05        19.00        36.00        26.99         0.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3846 
       35.05        25.02         1.02        17.98        15.95        17.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
       27.02        18.05        31.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       26.01        27.02        27.02         7.96        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R 
       30.02        34.03        18.05        17.03        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01P 
       17.03        21.99        34.98        15.02         0.99        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F 
        1.02         1.02        33.04        35.01        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-3400 TCGA-AF-3913 
        2.01         5.03        16.31         0.95        12.72        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
       36.03        32.02         1.02        24.00        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 TCGA-AG-3883 
        6.05        15.95        19.99        19.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4007 
       17.03        35.01        14.01        48.03        36.03         1.02 
TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 
       20.98        37.02         9.07        12.00        64.01         1.94 
TCGA-AG-A02G TCGA-AG-A036 
       38.96       117.11 

  KRAS MUTATED KRAS WILD-TYPE 
          0.92           0.95 
  KRAS MUTATED KRAS WILD-TYPE 
         70.03         117.11 
  KRAS MUTATED KRAS WILD-TYPE 
        21.995         19.990 
[1] "0.9 - 70.0 (22.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.5"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  KRAS MUTATED   59 37
  KRAS WILD-TYPE 94 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     59   37
  KRAS WILD-TYPE   94   31
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  COLON            59             94
  RECTUM           37             31
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KRAS MUTATED        24       11        26         1         8          1
  KRAS WILD-TYPE      25        9        31         3        10          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED            7          7       10         1
  KRAS WILD-TYPE         13         13       21         0
D3V4, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              24             25
  STAGE II             11              9
  STAGE IIA            26             31
  STAGE IIB             1              3
  STAGE III             8             10
  STAGE IIIA            1              1
  STAGE IIIB            7             13
  STAGE IIIC            7             13
  STAGE IV             10             21
  STAGE IVA             1              0
[1] 10  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
  KRAS MUTATED    6 21 65  5
  KRAS WILD-TYPE  3 26 84 13
D3V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            6              3
  T2           21             26
  T3           65             84
  T4            5             13
[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
  KRAS MUTATED   64 16 17
  KRAS WILD-TYPE 69 28 29
D3V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           64             69
  N1           16             28
  N2           17             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  KRAS MUTATED    85  10   1
  KRAS WILD-TYPE 104  21   0
D3V7, multiclass
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  M0            85            104
  M1            10             21
  M1A            1              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                cls
clus              0  1
  KRAS MUTATED   45 52
  KRAS WILD-TYPE 62 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     45   52
  KRAS WILD-TYPE   62   64
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           45             62
  MALE             52             64
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRAS MUTATED                     49                             9
  KRAS WILD-TYPE                   81                            13
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRAS MUTATED                      29                              6
  KRAS WILD-TYPE                    28                              2
D3V9, multiclass
                                clus
vv                               KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                     49             81
  COLON MUCINOUS ADENOCARCINOMA             9             13
  RECTAL ADENOCARCINOMA                    29             28
  RECTAL MUCINOUS ADENOCARCINOMA            6              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   88  0  7  1
  KRAS WILD-TYPE 99  2 20  0
D3V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           88             99
  R1            0              2
  R2            7             20
  RX            1              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"
D3V11, continuous

Clustering(4) Variable = NRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    15   4
  NRAS WILD-TYPE 154  31
  NRAS MUTATED NRAS WILD-TYPE 
            19            185 
  NRAS MUTATED NRAS WILD-TYPE 
             4             31 
$`NRAS MUTATED`
TCGA-A6-2678 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3819 TCGA-AA-3864 
       42.28        21.01        20.98         2.01        25.02        53.00 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A01V 
       50.99        13.05        26.01        34.03         4.01        35.01 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AF-2691 TCGA-AF-3913 TCGA-AG-3892 TCGA-AG-3894 
       39.06        39.98        43.04        10.39        13.02        14.01 
TCGA-AG-A01L 
       12.00 

$`NRAS WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        23.38        17.79        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       29.95        23.01        19.99        13.94        19.99        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       20.98        34.03         2.01        16.08        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01        37.02        51.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        41.00        39.98        18.05        40.96        16.31 
TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 
        0.95        17.95        13.55        12.72        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  NRAS MUTATED NRAS WILD-TYPE 
          2.01           0.92 
  NRAS MUTATED NRAS WILD-TYPE 
         53.00         117.11 
  NRAS MUTATED NRAS WILD-TYPE 
         25.02          19.99 
[1] "2.0 - 53.0 (25.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1"  
D4V2, continuous
D4V3, binary
                cls
clus               0   1
  NRAS MUTATED    15   5
  NRAS WILD-TYPE 138  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     15    5
  NRAS WILD-TYPE  138   63
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  COLON            15            138
  RECTUM            5             63
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  NRAS MUTATED         6        2         2         1         1          1
  NRAS WILD-TYPE      43       18        55         3        17          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED            2          1        4         0
  NRAS WILD-TYPE         18         19       27         1
D4V4, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               6             43
  STAGE II              2             18
  STAGE IIA             2             55
  STAGE IIB             1              3
  STAGE III             1             17
  STAGE IIIA            1              1
  STAGE IIIB            2             18
  STAGE IIIC            1             19
  STAGE IV              4             27
  STAGE IVA             0              1
[1] 10  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
  NRAS MUTATED     2   5  11   2
  NRAS WILD-TYPE   7  42 138  16
D4V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            2              7
  T2            5             42
  T3           11            138
  T4            2             16
[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
  NRAS MUTATED    11   8   1
  NRAS WILD-TYPE 122  36  45
D4V6, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           11            122
  N1            8             36
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  NRAS MUTATED    16   4   0
  NRAS WILD-TYPE 173  27   1
D4V7, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  M0            16            173
  M1             4             27
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                cls
clus               0   1
  NRAS MUTATED     5  15
  NRAS WILD-TYPE 102 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5   15
  NRAS WILD-TYPE  102  101
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            5            102
  MALE             15            101
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NRAS MUTATED                     13                             2
  NRAS WILD-TYPE                  117                            20
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NRAS MUTATED                       5                              0
  NRAS WILD-TYPE                    52                              8
D4V9, multiclass
                                clus
vv                               NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                     13            117
  COLON MUCINOUS ADENOCARCINOMA             2             20
  RECTAL ADENOCARCINOMA                     5             52
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    16   0   4   0
  NRAS WILD-TYPE 171   2  23   1
D4V10, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           16            171
  R1            0              2
  R2            4             23
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous

Clustering(5) Variable = SMAD4 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    18   5
  SMAD4 WILD-TYPE 151  30
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             23             181 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              5              30 
$`SMAD4 MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3555 
       23.38        42.28        24.03        37.05        19.07        29.95 
TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3864 
       20.98         2.01        36.00         0.99         1.02        53.00 
TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A01D TCGA-AA-A02O TCGA-AG-3887 TCGA-AG-4005 
       13.05        18.05         0.99         0.92        36.95        14.04 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A02X 
       13.94        37.02         9.07        10.98        41.00 

$`SMAD4 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        17.79        15.52        34.65        33.34 
TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       36.53         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       13.02        24.00        17.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       26.99         0.99        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       39.06        51.98        39.98         2.01         5.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C 
       28.04        36.03         1.02        17.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W 
       25.97        23.01        15.95        36.03        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       64.01        49.97         1.94        38.96        61.97        38.04 
TCGA-AG-A036 
      117.11 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.92            0.92 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          53.00          117.11 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          19.07           20.98 
[1] "0.9 - 53.0 (19.1)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
                 cls
clus                0   1
  SMAD4 MUTATED    18   8
  SMAD4 WILD-TYPE 135  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     18    8
  SMAD4 WILD-TYPE  135   60
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON             18             135
  RECTUM             8              60
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD4 MUTATED         5        3         7         1         3          0
  SMAD4 WILD-TYPE      44       17        50         3        15          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED            2          1        4         0
  SMAD4 WILD-TYPE         18         19       27         1
D5V4, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                5              44
  STAGE II               3              17
  STAGE IIA              7              50
  STAGE IIB              1               3
  STAGE III              3              15
  STAGE IIIA             0               2
  STAGE IIIB             2              18
  STAGE IIIC             1              19
  STAGE IV               4              27
  STAGE IVA              0               1
[1] 10  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
  SMAD4 MUTATED     0   5  19   2
  SMAD4 WILD-TYPE   9  42 130  16
D5V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             0               9
  T2             5              42
  T3            19             130
  T4             2              16
[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
  SMAD4 MUTATED    16   5   5
  SMAD4 WILD-TYPE 117  39  41
D5V6, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            16             117
  N1             5              39
  N2             5              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  SMAD4 MUTATED    22   4   0
  SMAD4 WILD-TYPE 167  27   1
D5V7, multiclass
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  M0             22             167
  M1              4              27
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    13  13
  SMAD4 WILD-TYPE  94 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     13   13
  SMAD4 WILD-TYPE   94  103
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            13              94
  MALE              13             103
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAD4 MUTATED                     14                             4
  SMAD4 WILD-TYPE                  116                            18
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAD4 MUTATED                       4                              4
  SMAD4 WILD-TYPE                    53                              4
D5V9, multiclass
                                clus
vv                               SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                      14             116
  COLON MUCINOUS ADENOCARCINOMA              4              18
  RECTAL ADENOCARCINOMA                      4              53
  RECTAL MUCINOUS ADENOCARCINOMA             4               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"
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    22   0   4   0
  SMAD4 WILD-TYPE 165   2  23   1
D5V10, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            22             165
  R1             0               2
  R2             4              23
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    25   7
  FBXW7 WILD-TYPE 144  28
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             32             172 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              7              28 
$`FBXW7 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-3807 TCGA-AA-3516 TCGA-AA-3518 
       46.65        23.38        17.79        34.65        13.02         1.02 
TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3831 
       36.03         0.99        19.99         0.92         5.98        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3949 TCGA-AA-3982 TCGA-AA-A00J 
       15.95        38.99         0.99        26.01        27.02        18.05 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A03F 
       31.00         1.02        35.01        37.02        39.06        18.05 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
        2.01         6.05        15.95        13.02        48.03        20.98 
TCGA-AG-A011 TCGA-AG-A02N 
       37.02        61.97 

$`FBXW7 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 
       43.76        42.28        15.52        33.34        36.53         1.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
       38.99         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       29.95        23.01        20.98        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3842 
        0.99        35.05         0.99        25.02         1.02        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       33.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 
       38.07         1.02        33.04        35.01        26.01        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
       34.03        50.04        12.03         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        41.00        38.04       117.11 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.92            0.92 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          61.97          117.11 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          19.02           20.98 
[1] "0.9 - 62.0 (19.0)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
                 cls
clus                0   1
  FBXW7 MUTATED    29   9
  FBXW7 WILD-TYPE 124  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     29    9
  FBXW7 WILD-TYPE  124   59
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON             29             124
  RECTUM             9              59
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FBXW7 MUTATED         4        6        12         1         5          0
  FBXW7 WILD-TYPE      45       14        45         3        13          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED            4          6        0         0
  FBXW7 WILD-TYPE         16         14       31         1
D6V4, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                4              45
  STAGE II               6              14
  STAGE IIA             12              45
  STAGE IIB              1               3
  STAGE III              5              13
  STAGE IIIA             0               2
  STAGE IIIB             4              16
  STAGE IIIC             6              14
  STAGE IV               0              31
  STAGE IVA              0               1
[1] 10  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     1   3  31   3
  FBXW7 WILD-TYPE   8  44 118  15
D6V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             1               8
  T2             3              44
  T3            31             118
  T4             3              15
[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
  FBXW7 MUTATED    23   6   9
  FBXW7 WILD-TYPE 110  38  37
D6V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            23             110
  N1             6              38
  N2             9              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  FBXW7 MUTATED    38   0   0
  FBXW7 WILD-TYPE 151  31   1
D6V7, multiclass
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  M0             38             151
  M1              0              31
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                 cls
clus               0  1
  FBXW7 MUTATED   21 17
  FBXW7 WILD-TYPE 86 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     21   17
  FBXW7 WILD-TYPE   86   99
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            21              86
  MALE              17              99
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXW7 MUTATED                     20                             9
  FBXW7 WILD-TYPE                  110                            13
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXW7 MUTATED                       7                              1
  FBXW7 WILD-TYPE                    50                              7
D6V9, multiclass
                                clus
vv                               FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                      20             110
  COLON MUCINOUS ADENOCARCINOMA              9              13
  RECTAL ADENOCARCINOMA                      7              50
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    35   0   0   0
  FBXW7 WILD-TYPE 152   2  27   1
D6V10, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            35             152
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous

Clustering(7) Variable = SMAD2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED    11   3
  SMAD2 WILD-TYPE 158  32
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             14             190 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              3              32 
$`SMAD2 MUTATED`
TCGA-AA-3520 TCGA-AA-3696 TCGA-AA-3842 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       24.03         5.03        37.02        53.00        25.02         4.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AG-3608 TCGA-AG-3890 TCGA-AG-A002 
       35.01        39.06        51.98        15.95        17.03        20.98 
TCGA-AG-A011 TCGA-AG-A01W 
       37.02        70.03 

$`SMAD2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           4.01            0.92 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          70.03          117.11 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         30.015          19.990 
[1] "4.0 - 70.0 (30.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                 cls
clus                0   1
  SMAD2 MUTATED    10   5
  SMAD2 WILD-TYPE 143  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     10    5
  SMAD2 WILD-TYPE  143   63
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON             10             143
  RECTUM             5              63
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD2 MUTATED         3        5         2         1         0          1
  SMAD2 WILD-TYPE      46       15        55         3        18          1
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED            0          0        2         0
  SMAD2 WILD-TYPE         20         20       29         1
D7V4, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                3              46
  STAGE II               5              15
  STAGE IIA              2              55
  STAGE IIB              1               3
  STAGE III              0              18
  STAGE IIIA             1               1
  STAGE IIIB             0              20
  STAGE IIIC             0              20
  STAGE IV               2              29
  STAGE IVA              0               1
[1] 10  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
  SMAD2 MUTATED     0   5   8   2
  SMAD2 WILD-TYPE   9  42 141  16
D7V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               9
  T2             5              42
  T3             8             141
  T4             2              16
[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
  SMAD2 MUTATED    12   2   1
  SMAD2 WILD-TYPE 121  42  45
D7V6, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0            12             121
  N1             2              42
  N2             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  SMAD2 MUTATED    12   2   0
  SMAD2 WILD-TYPE 177  29   1
D7V7, multiclass
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  M0             12             177
  M1              2              29
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     5  10
  SMAD2 WILD-TYPE 102 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      5   10
  SMAD2 WILD-TYPE  102  106
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             5             102
  MALE              10             106
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAD2 MUTATED                      7                             3
  SMAD2 WILD-TYPE                  123                            19
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAD2 MUTATED                       5                              0
  SMAD2 WILD-TYPE                    52                              8
D7V9, multiclass
                                clus
vv                               SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             123
  COLON MUCINOUS ADENOCARCINOMA              3              19
  RECTAL ADENOCARCINOMA                      5              52
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED    12   0   2   0
  SMAD2 WILD-TYPE 175   2  25   1
D7V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0            12             175
  R1             0               2
  R2             2              25
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous

Clustering(8) Variable = FAM123B MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  FAM123B MUTATED    13   7
  FAM123B WILD-TYPE 156  28
  FAM123B MUTATED FAM123B WILD-TYPE 
               20               184 
  FAM123B MUTATED FAM123B WILD-TYPE 
                7                28 
$`FAM123B MUTATED`
TCGA-A6-3808 TCGA-AA-3516 TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3666 
       33.34        13.02        19.07        33.99        17.95         2.01 
TCGA-AA-3680 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3977 
       11.01         1.02        53.00        27.02        12.99        25.02 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01D TCGA-AG-3584 TCGA-AG-3892 TCGA-AG-3896 
       38.04        34.98         0.99        24.00        13.02         1.02 
TCGA-AG-A02G TCGA-AG-A02N 
       38.96        61.97 

$`FAM123B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       34.65        36.53         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       19.99        13.94        19.99        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
        0.99        31.07        31.07        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        41.00        38.04       117.11 

  FAM123B MUTATED FAM123B WILD-TYPE 
             0.99              0.92 
  FAM123B MUTATED FAM123B WILD-TYPE 
            61.97            117.11 
  FAM123B MUTATED FAM123B WILD-TYPE 
           21.535            20.485 
[1] "1.0 - 62.0 (21.5)"  "0.9 - 117.1 (20.5)"
[1] "hr=" "2.3"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  FAM123B MUTATED    19   5
  FAM123B WILD-TYPE 134  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     19    5
  FAM123B WILD-TYPE  134   63
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  COLON               19               134
  RECTUM               5                63
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FAM123B MUTATED         4        3         7         1         2          0
  FAM123B WILD-TYPE      45       17        50         3        16          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM123B MUTATED            0          2        4         0
  FAM123B WILD-TYPE         20         18       27         1
D8V4, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  4                45
  STAGE II                 3                17
  STAGE IIA                7                50
  STAGE IIB                1                 3
  STAGE III                2                16
  STAGE IIIA               0                 2
  STAGE IIIB               0                20
  STAGE IIIC               2                18
  STAGE IV                 4                27
  STAGE IVA                0                 1
[1] 10  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
  FAM123B MUTATED     1   5  15   3
  FAM123B WILD-TYPE   8  42 134  15
D8V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               1                 8
  T2               5                42
  T3              15               134
  T4               3                15
[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
  FAM123B MUTATED    16   2   6
  FAM123B WILD-TYPE 117  42  40
D8V6, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0              16               117
  N1               2                42
  N2               6                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A
  FAM123B MUTATED    19   4   0
  FAM123B WILD-TYPE 170  27   1
D8V7, multiclass
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  M0               19               170
  M1                4                27
  M1A               0                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED    12  12
  FAM123B WILD-TYPE  95 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     12   12
  FAM123B WILD-TYPE   95  104
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              12                95
  MALE                12               104
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM123B MUTATED                     16                             3
  FAM123B WILD-TYPE                  114                            19
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM123B MUTATED                       5                              0
  FAM123B WILD-TYPE                    52                              8
D8V9, multiclass
                                clus
vv                               FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                        16               114
  COLON MUCINOUS ADENOCARCINOMA                3                19
  RECTAL ADENOCARCINOMA                        5                52
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    18   0   4   0
  FAM123B WILD-TYPE 169   2  23   1
D8V10, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              18               169
  R1               0                 2
  R2               4                23
  RX               0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    23   6
  PIK3CA WILD-TYPE 146  29
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              29              175 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               6               29 
$`PIK3CA MUTATED`
TCGA-A6-3808 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       33.34        50.04         5.03         0.99        35.05         0.99 
TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3939 
       38.99         0.99        53.00        17.03        31.00        12.99 
TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
       33.01        34.03        25.02         4.01        34.98        31.00 
TCGA-AA-A01K TCGA-AA-A01V TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       31.00        35.01         0.92        39.98        18.05        40.96 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-A00H TCGA-AG-A020 TCGA-AG-A02N 
        0.99        36.95        25.97        10.98        61.97 

$`PIK3CA WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       34.65        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 
       19.99        54.02         2.01        14.01         0.92        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93        17.03        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        31.07        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       18.05         2.01        24.00        26.01         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02         0.99        32.02        12.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       41.00        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3882 
       15.95        19.99        19.99         7.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       64.01        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 
      117.11 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.92             0.92 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           61.97           117.11 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           31.00            19.99 
[1] "0.9 - 62.0 (31.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    26   7
  PIK3CA WILD-TYPE 127  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     26    7
  PIK3CA WILD-TYPE  127   61
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON              26              127
  RECTUM              7               61
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PIK3CA MUTATED         8        5        10         3         2          0
  PIK3CA WILD-TYPE      41       15        47         1        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIK3CA MUTATED            1          2        1         0
  PIK3CA WILD-TYPE         19         18       30         1
D9V4, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 8               41
  STAGE II                5               15
  STAGE IIA              10               47
  STAGE IIB               3                1
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              1               19
  STAGE IIIC              2               18
  STAGE IV                1               30
  STAGE IVA               0                1
[1] 10  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     1   8  21   3
  PIK3CA WILD-TYPE   8  39 128  15
D9V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1                8
  T2              8               39
  T3             21              128
  T4              3               15
[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
  PIK3CA MUTATED    27   3   3
  PIK3CA WILD-TYPE 106  41  43
D9V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             27              106
  N1              3               41
  N2              3               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  PIK3CA MUTATED    31   1   0
  PIK3CA WILD-TYPE 158  30   1
D9V7, multiclass
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              31              158
  M1               1               30
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                  cls
clus                0  1
  PIK3CA MUTATED   15 18
  PIK3CA WILD-TYPE 92 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     15   18
  PIK3CA WILD-TYPE   92   98
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             15               92
  MALE               18               98
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3CA MUTATED                     20                             6
  PIK3CA WILD-TYPE                  110                            16
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3CA MUTATED                       4                              3
  PIK3CA WILD-TYPE                    53                              5
D9V9, multiclass
                                clus
vv                               PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                       20              110
  COLON MUCINOUS ADENOCARCINOMA               6               16
  RECTAL ADENOCARCINOMA                       4               53
  RECTAL MUCINOUS ADENOCARCINOMA              3                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"
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    31   0   1   0
  PIK3CA WILD-TYPE 156   2  26   1
D9V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             31              156
  R1              0                2
  R2              1               26
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous

Clustering(10) Variable = TCF7L2 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  TCF7L2 MUTATED    14   1
  TCF7L2 WILD-TYPE 155  34
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              15              189 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               1               34 
$`TCF7L2 MUTATED`
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A010 
        0.92        50.04        20.98        25.02        18.05        34.98 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AF-2692 TCGA-AG-3582 TCGA-AG-3726 TCGA-AG-3882 
       31.00        33.04        13.55         1.02         7.99        19.99 
TCGA-AG-3898 TCGA-AG-4007 TCGA-AG-A032 
       48.03         1.02        38.04 

$`TCF7L2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       13.94        19.99        54.02         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01         2.01        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        41.00        39.98        18.05        40.96        16.31 
TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
        0.95        17.95        43.04        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 
        6.05         0.99        15.95        19.99        19.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       61.97        41.00       117.11 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.92             0.92 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           50.04           117.11 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           20.98            19.99 
[1] "0.9 - 50.0 (21.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "2.6"
D10V2, continuous
D10V3, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    11   6
  TCF7L2 WILD-TYPE 142  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     11    6
  TCF7L2 WILD-TYPE  142   62
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON              11              142
  RECTUM              6               62
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TCF7L2 MUTATED         3        2         4         1         2          0
  TCF7L2 WILD-TYPE      46       18        53         3        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7L2 MUTATED            2          0        3         0
  TCF7L2 WILD-TYPE         18         20       28         1
D10V4, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 3               46
  STAGE II                2               18
  STAGE IIA               4               53
  STAGE IIB               1                3
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              2               18
  STAGE IIIC              0               20
  STAGE IV                3               28
  STAGE IVA               0                1
[1] 10  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
  TCF7L2 MUTATED     0   5  10   3
  TCF7L2 WILD-TYPE   9  42 139  15
D10V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                9
  T2              5               42
  T3             10              139
  T4              3               15
[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
  TCF7L2 MUTATED    11   4   3
  TCF7L2 WILD-TYPE 122  40  43
D10V6, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0             11              122
  N1              4               40
  N2              3               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  TCF7L2 MUTATED    14   3   0
  TCF7L2 WILD-TYPE 175  28   1
D10V7, multiclass
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  M0              14              175
  M1               3               28
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    10   8
  TCF7L2 WILD-TYPE  97 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     10    8
  TCF7L2 WILD-TYPE   97  108
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE             10               97
  MALE                8              108
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCF7L2 MUTATED                     11                             0
  TCF7L2 WILD-TYPE                  119                            22
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCF7L2 MUTATED                       6                              0
  TCF7L2 WILD-TYPE                    51                              8
D10V9, multiclass
                                clus
vv                               TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON ADENOCARCINOMA                       11              119
  COLON MUCINOUS ADENOCARCINOMA               0               22
  RECTAL ADENOCARCINOMA                       6               51
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCF7L2 MUTATED    14   0   3   0
  TCF7L2 WILD-TYPE 173   2  24   1
D10V10, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0             14              173
  R1              0                2
  R2              3               24
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous

Clustering(11) Variable = ARID1A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    16   3
  ARID1A WILD-TYPE 153  32
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              185 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               32 
$`ARID1A MUTATED`
TCGA-A6-2676 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3831 
       23.38         1.02        13.02        17.95        29.95        17.98 
TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00L TCGA-AA-A010 
       24.03        33.01        38.04        30.02        17.03        34.98 
TCGA-AA-A017 TCGA-AA-A01R TCGA-AG-3574 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A00H 
       15.02        35.01        36.03         0.99        13.02        25.97 
TCGA-AG-A025 
       49.97 

$`ARID1A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       33.34        36.53        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        13.02        24.00        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        13.94        19.99        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
        0.99        35.05         0.99        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        19.00        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        41.00        39.98        18.05        40.96        16.31 
TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
        0.95        17.95        43.04        13.55        12.72        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        7.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.92 
  ARID1A MUTATED ARID1A WILD-TYPE 
           49.97           117.11 
  ARID1A MUTATED ARID1A WILD-TYPE 
           24.03            19.99 
[1] "1.0 - 50.0 (24.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                  cls
clus                 0   1
  ARID1A MUTATED    15   5
  ARID1A WILD-TYPE 138  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     15    5
  ARID1A WILD-TYPE  138   63
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  COLON              15              138
  RECTUM              5               63
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ARID1A MUTATED         4        1         9         3         2          0
  ARID1A WILD-TYPE      45       19        48         1        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID1A MUTATED            0          0        1         0
  ARID1A WILD-TYPE         20         20       30         1
D11V4, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 4               45
  STAGE II                1               19
  STAGE IIA               9               48
  STAGE IIB               3                1
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              0               20
  STAGE IIIC              0               20
  STAGE IV                1               30
  STAGE IVA               0                1
[1] 10  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
  ARID1A MUTATED     2   2  13   3
  ARID1A WILD-TYPE   7  45 136  15
D11V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2                7
  T2              2               45
  T3             13              136
  T4              3               15
[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
  ARID1A MUTATED    17   0   3
  ARID1A WILD-TYPE 116  44  43
D11V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             17              116
  N1              0               44
  N2              3               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  ARID1A MUTATED    19   1   0
  ARID1A WILD-TYPE 170  30   1
D11V7, multiclass
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  M0              19              170
  M1               1               30
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    12   8
  ARID1A WILD-TYPE  95 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     12    8
  ARID1A WILD-TYPE   95  108
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             12               95
  MALE                8              108
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARID1A MUTATED                     11                             4
  ARID1A WILD-TYPE                  119                            18
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARID1A MUTATED                       5                              0
  ARID1A WILD-TYPE                    52                              8
D11V9, multiclass
                                clus
vv                               ARID1A MUTATED ARID1A WILD-TYPE
  COLON ADENOCARCINOMA                       11              119
  COLON MUCINOUS ADENOCARCINOMA               4               18
  RECTAL ADENOCARCINOMA                       5               52
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    18   0   1   0
  ARID1A WILD-TYPE 169   2  26   1
D11V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             18              169
  R1              0                2
  R2              1               26
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous

Clustering(12) Variable = BRAF MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    14   5
  BRAF WILD-TYPE 155  30
  BRAF MUTATED BRAF WILD-TYPE 
            19            185 
  BRAF MUTATED BRAF WILD-TYPE 
             5             30 
$`BRAF MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3543 
       46.65        23.38        13.02         8.05        12.99         0.99 
TCGA-AA-3664 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3947 
       54.02         0.99         1.02        15.95        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01P 
       26.01         2.01        19.00        18.05         0.99        38.07 
TCGA-AG-3578 
       32.02 

$`BRAF WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        17.79        42.28        15.52        34.65        33.34 
TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       36.53         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        26.01        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       13.94        19.99         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        17.98        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       18.05         2.01        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       12.72        10.39        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 
       19.99        19.99         7.99         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  BRAF MUTATED BRAF WILD-TYPE 
          0.99           0.92 
  BRAF MUTATED BRAF WILD-TYPE 
         54.02         117.11 
  BRAF MUTATED BRAF WILD-TYPE 
         18.05          20.98 
[1] "1.0 - 54.0 (18.1)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.8"
D12V2, continuous
D12V3, binary
                cls
clus               0   1
  BRAF MUTATED    20   1
  BRAF WILD-TYPE 133  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     20    1
  BRAF WILD-TYPE  133   67
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  COLON            20            133
  RECTUM            1             67
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BRAF MUTATED         4        3         3         2         2          0
  BRAF WILD-TYPE      45       17        54         2        16          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED            4          2        1         0
  BRAF WILD-TYPE         16         18       30         1
D12V4, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               4             45
  STAGE II              3             17
  STAGE IIA             3             54
  STAGE IIB             2              2
  STAGE III             2             16
  STAGE IIIA            0              2
  STAGE IIIB            4             16
  STAGE IIIC            2             18
  STAGE IV              1             30
  STAGE IVA             0              1
[1] 10  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
  BRAF MUTATED     1   3  12   5
  BRAF WILD-TYPE   8  44 137  13
D12V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            1              8
  T2            3             44
  T3           12            137
  T4            5             13
[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
  BRAF MUTATED    12   5   4
  BRAF WILD-TYPE 121  39  42
D12V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           12            121
  N1            5             39
  N2            4             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  BRAF MUTATED    20   1   0
  BRAF WILD-TYPE 169  30   1
D12V7, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  M0            20            169
  M1             1             30
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                cls
clus               0   1
  BRAF MUTATED    15   6
  BRAF WILD-TYPE  92 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     15    6
  BRAF WILD-TYPE   92  110
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           15             92
  MALE              6            110
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRAF MUTATED                     10                            10
  BRAF WILD-TYPE                  120                            12
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRAF MUTATED                       0                              1
  BRAF WILD-TYPE                    57                              7
D12V9, multiclass
                                clus
vv                               BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                     10            120
  COLON MUCINOUS ADENOCARCINOMA            10             12
  RECTAL ADENOCARCINOMA                     0             57
  RECTAL MUCINOUS ADENOCARCINOMA            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    18   0   1   0
  BRAF WILD-TYPE 169   2  26   1
D12V10, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           18            169
  R1            0              2
  R2            1             26
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous

Clustering(13) Variable = MGC42105 MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                  0   1
  MGC42105 MUTATED     9   1
  MGC42105 WILD-TYPE 160  34
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                10                194 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                 1                 34 
$`MGC42105 MUTATED`
TCGA-AA-3522 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3710 TCGA-AA-3842 
       37.05        17.95        29.95        20.98        26.99        37.02 
TCGA-AA-3848 TCGA-AA-3877 TCGA-AA-3977 TCGA-AG-A002 
        0.99        31.00        25.02        20.98 

$`MGC42105 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 
       23.01        19.99        13.94        19.99        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 
        5.98        37.05        19.00        36.00         5.03         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       15.95        38.99        14.93        17.03        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  MGC42105 MUTATED MGC42105 WILD-TYPE 
              0.99               0.92 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
             37.05             117.11 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
            26.005             19.990 
[1] "1.0 - 37.0 (26.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.8"
D13V2, continuous
D13V3, binary
                    cls
clus                   0   1
  MGC42105 MUTATED    10   1
  MGC42105 WILD-TYPE 143  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC42105 MUTATED     10    1
  MGC42105 WILD-TYPE  143   67
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  COLON                10                143
  RECTUM                1                 67
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MGC42105 MUTATED         3        0         5         0         0          1
  MGC42105 WILD-TYPE      46       20        52         4        18          1
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGC42105 MUTATED            0          1        0         0
  MGC42105 WILD-TYPE         20         19       31         1
D13V4, multiclass
            clus
vv           MGC42105 MUTATED MGC42105 WILD-TYPE
  STAGE I                   3                 46
  STAGE II                  0                 20
  STAGE IIA                 5                 52
  STAGE IIB                 0                  4
  STAGE III                 0                 18
  STAGE IIIA                1                  1
  STAGE IIIB                0                 20
  STAGE IIIC                1                 19
  STAGE IV                  0                 31
  STAGE IVA                 0                  1
[1] 10  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
  MGC42105 MUTATED     1   4   6   0
  MGC42105 WILD-TYPE   8  43 143  18
D13V5, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  T1                1                  8
  T2                4                 43
  T3                6                143
  T4                0                 18
[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
  MGC42105 MUTATED     9   1   1
  MGC42105 WILD-TYPE 124  43  45
D13V6, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  N0                9                124
  N1                1                 43
  N2                1                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A
  MGC42105 MUTATED    10   0   0
  MGC42105 WILD-TYPE 179  31   1
D13V7, multiclass
     clus
vv    MGC42105 MUTATED MGC42105 WILD-TYPE
  M0                10                179
  M1                 0                 31
  M1A                0                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                    cls
clus                   0   1
  MGC42105 MUTATED     6   5
  MGC42105 WILD-TYPE 101 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC42105 MUTATED      6    5
  MGC42105 WILD-TYPE  101  111
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  FEMALE                6                101
  MALE                  5                111
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MGC42105 MUTATED                      8                             2
  MGC42105 WILD-TYPE                  122                            20
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MGC42105 MUTATED                       1                              0
  MGC42105 WILD-TYPE                    56                              8
D13V9, multiclass
                                clus
vv                               MGC42105 MUTATED MGC42105 WILD-TYPE
  COLON ADENOCARCINOMA                          8                122
  COLON MUCINOUS ADENOCARCINOMA                 2                 20
  RECTAL ADENOCARCINOMA                         1                 56
  RECTAL MUCINOUS ADENOCARCINOMA                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  MGC42105 MUTATED     9   0   1   0
  MGC42105 WILD-TYPE 178   2  26   1
D13V10, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  R0                9                178
  R1                0                  2
  R2                1                 26
  RX                0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous

Clustering(14) Variable = ACVR1B MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED    10   3
  ACVR1B WILD-TYPE 159  32
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              191 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               3               32 
$`ACVR1B MUTATED`
TCGA-A6-3807 TCGA-AA-3715 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3994 
       34.65         0.99        17.98        15.95        31.00        27.02 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A03F 
       18.05        34.98        35.01        51.98         5.03        18.05 
TCGA-AG-A01L 
       12.00 

$`ACVR1B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02         1.02        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.06        39.98         2.01         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            0.99             0.92 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           51.98           117.11 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           18.05            20.98 
[1] "1.0 - 52.0 (18.1)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.4"
D14V2, continuous
D14V3, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    13   1
  ACVR1B WILD-TYPE 140  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     13    1
  ACVR1B WILD-TYPE  140   67
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON              13              140
  RECTUM              1               67
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ACVR1B MUTATED         1        3         2         1         2          0
  ACVR1B WILD-TYPE      48       17        55         3        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACVR1B MUTATED            3          1        1         0
  ACVR1B WILD-TYPE         17         19       30         1
D14V4, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1               48
  STAGE II                3               17
  STAGE IIA               2               55
  STAGE IIB               1                3
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              3               17
  STAGE IIIC              1               19
  STAGE IV                1               30
  STAGE IVA               0                1
[1] 10  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
  ACVR1B MUTATED     1   0  10   3
  ACVR1B WILD-TYPE   8  47 139  15
D14V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              1                8
  T2              0               47
  T3             10              139
  T4              3               15
[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
  ACVR1B MUTATED     8   3   3
  ACVR1B WILD-TYPE 125  41  43
D14V6, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              8              125
  N1              3               41
  N2              3               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  ACVR1B MUTATED    13   1   0
  ACVR1B WILD-TYPE 176  30   1
D14V7, multiclass
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  M0              13              176
  M1               1               30
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     7   7
  ACVR1B WILD-TYPE 100 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      7    7
  ACVR1B WILD-TYPE  100  109
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              7              100
  MALE                7              109
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACVR1B MUTATED                      8                             5
  ACVR1B WILD-TYPE                  122                            17
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACVR1B MUTATED                       1                              0
  ACVR1B WILD-TYPE                    56                              8
D14V9, multiclass
                                clus
vv                               ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON ADENOCARCINOMA                        8              122
  COLON MUCINOUS ADENOCARCINOMA               5               17
  RECTAL ADENOCARCINOMA                       1               56
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED    13   0   1   0
  ACVR1B WILD-TYPE 174   2  26   1
D14V10, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             13              174
  R1              0                2
  R2              1               26
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous

Clustering(15) Variable = CDC27 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED     9   3
  CDC27 WILD-TYPE 160  32
  CDC27 MUTATED CDC27 WILD-TYPE 
             12             192 
  CDC27 MUTATED CDC27 WILD-TYPE 
              3              32 
$`CDC27 MUTATED`
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00E TCGA-AA-A00K 
        1.02         1.02        29.95         0.99        30.02        18.05 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AG-3583 TCGA-AG-3892 TCGA-AG-A002 
       34.98        38.07         1.02         2.01        13.02        20.98 

$`CDC27 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       34.65        33.34        36.53        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        34.03        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.99            0.92 
  CDC27 MUTATED CDC27 WILD-TYPE 
          38.07          117.11 
  CDC27 MUTATED CDC27 WILD-TYPE 
         15.535          20.980 
[1] "1.0 - 38.1 (15.5)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "2.1"
D15V2, continuous
D15V3, binary
                 cls
clus                0   1
  CDC27 MUTATED    10   3
  CDC27 WILD-TYPE 143  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     10    3
  CDC27 WILD-TYPE  143   65
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  COLON             10             143
  RECTUM             3              65
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CDC27 MUTATED         3        1         5         1         2          0
  CDC27 WILD-TYPE      46       19        52         3        16          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC27 MUTATED            0          0        1         0
  CDC27 WILD-TYPE         20         20       30         1
D15V4, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                3              46
  STAGE II               1              19
  STAGE IIA              5              52
  STAGE IIB              1               3
  STAGE III              2              16
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             0              20
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  CDC27 MUTATED     1   2   9   1
  CDC27 WILD-TYPE   8  45 140  17
D15V5, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             1               8
  T2             2              45
  T3             9             140
  T4             1              17
[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
  CDC27 MUTATED    10   1   2
  CDC27 WILD-TYPE 123  43  44
D15V6, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  N0            10             123
  N1             1              43
  N2             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  CDC27 MUTATED    12   1   0
  CDC27 WILD-TYPE 177  30   1
D15V7, multiclass
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  M0             12             177
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                 cls
clus                0   1
  CDC27 MUTATED     9   4
  CDC27 WILD-TYPE  98 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      9    4
  CDC27 WILD-TYPE   98  112
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             9              98
  MALE               4             112
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC27 MUTATED                      9                             1
  CDC27 WILD-TYPE                  121                            21
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC27 MUTATED                       2                              1
  CDC27 WILD-TYPE                    55                              7
D15V9, multiclass
                                clus
vv                               CDC27 MUTATED CDC27 WILD-TYPE
  COLON ADENOCARCINOMA                       9             121
  COLON MUCINOUS ADENOCARCINOMA              1              21
  RECTAL ADENOCARCINOMA                      2              55
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC27 MUTATED    12   0   1   0
  CDC27 WILD-TYPE 175   2  26   1
D15V10, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0            12             175
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous

Clustering(16) Variable = KIAA1804 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  KIAA1804 MUTATED    12   1
  KIAA1804 WILD-TYPE 157  34
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                13                191 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                 34 
$`KIAA1804 MUTATED`
TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3966 TCGA-AA-A010 TCGA-AF-2691 
       29.95         0.92        19.00         2.01        34.98        43.04 
TCGA-AG-3582 TCGA-AG-3598 TCGA-AG-3727 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 
        1.02        50.04         0.99        48.03        20.98        13.94 
TCGA-AG-A02N 
       61.97 

$`KIAA1804 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2692 
       18.05        40.96        16.31         0.95        17.95        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       19.99         7.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        41.00        38.04       117.11 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.92               0.92 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             61.97             117.11 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             20.98              19.99 
[1] "0.9 - 62.0 (21.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "2.5"
D16V2, continuous
D16V3, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     6   9
  KIAA1804 WILD-TYPE 147  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      6    9
  KIAA1804 WILD-TYPE  147   59
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON                 6                147
  RECTUM                9                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KIAA1804 MUTATED         3        1         5         1         2          0
  KIAA1804 WILD-TYPE      46       19        52         3        16          2
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIAA1804 MUTATED            0          1        2         0
  KIAA1804 WILD-TYPE         20         19       29         1
D16V4, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   3                 46
  STAGE II                  1                 19
  STAGE IIA                 5                 52
  STAGE IIB                 1                  3
  STAGE III                 2                 16
  STAGE IIIA                0                  2
  STAGE IIIB                0                 20
  STAGE IIIC                1                 19
  STAGE IV                  2                 29
  STAGE IVA                 0                  1
[1] 10  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
  KIAA1804 MUTATED     1   2  11   1
  KIAA1804 WILD-TYPE   8  45 138  17
D16V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                1                  8
  T2                2                 45
  T3               11                138
  T4                1                 17
[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
  KIAA1804 MUTATED    10   4   1
  KIAA1804 WILD-TYPE 123  40  45
D16V6, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0               10                123
  N1                4                 40
  N2                1                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A
  KIAA1804 MUTATED    13   2   0
  KIAA1804 WILD-TYPE 176  29   1
D16V7, multiclass
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  M0                13                176
  M1                 2                 29
  M1A                0                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     9   6
  KIAA1804 WILD-TYPE  98 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      9    6
  KIAA1804 WILD-TYPE   98  110
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE                9                 98
  MALE                  6                110
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1804 MUTATED                      4                             2
  KIAA1804 WILD-TYPE                  126                            20
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1804 MUTATED                       8                              1
  KIAA1804 WILD-TYPE                    49                              7
D16V9, multiclass
                                clus
vv                               KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON ADENOCARCINOMA                          4                126
  COLON MUCINOUS ADENOCARCINOMA                 2                 20
  RECTAL ADENOCARCINOMA                         8                 49
  RECTAL MUCINOUS ADENOCARCINOMA                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1804 MUTATED    12   0   2   0
  KIAA1804 WILD-TYPE 175   2  25   1
D16V10, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0               12                175
  R1                0                  2
  R2                2                 25
  RX                0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous

Clustering(17) Variable = PCDHGB1 MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  PCDHGB1 MUTATED     5   2
  PCDHGB1 WILD-TYPE 164  33
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                7               197 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                2                33 
$`PCDHGB1 MUTATED`
TCGA-AA-3672 TCGA-AA-3848 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
        0.92         0.99        53.00         2.01         4.01        34.98 
TCGA-AG-A032 
       38.04 

$`PCDHGB1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        19.99        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93        17.03        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
        1.94        38.96        61.97        41.00       117.11 

  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
             0.92              0.92 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
            53.00            117.11 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
             4.01             20.98 
[1] "0.9 - 53.0 (4.0)"   "0.9 - 117.1 (21.0)"
[1] "hr=" "2.1"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  PCDHGB1 MUTATED     7   1
  PCDHGB1 WILD-TYPE 146  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB1 MUTATED      7    1
  PCDHGB1 WILD-TYPE  146   67
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  COLON                7               146
  RECTUM               1                67
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHGB1 MUTATED         0        1         2         2         1          0
  PCDHGB1 WILD-TYPE      49       19        55         2        17          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGB1 MUTATED            1          1        0         0
  PCDHGB1 WILD-TYPE         19         19       31         1
D17V4, multiclass
            clus
vv           PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  STAGE I                  0                49
  STAGE II                 1                19
  STAGE IIA                2                55
  STAGE IIB                2                 2
  STAGE III                1                17
  STAGE IIIA               0                 2
  STAGE IIIB               1                19
  STAGE IIIC               1                19
  STAGE IV                 0                31
  STAGE IVA                0                 1
[1] 10  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
  PCDHGB1 MUTATED     0   0   6   2
  PCDHGB1 WILD-TYPE   9  47 143  16
D17V5, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  T1               0                 9
  T2               0                47
  T3               6               143
  T4               2                16
[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
  PCDHGB1 MUTATED     5   2   1
  PCDHGB1 WILD-TYPE 128  42  45
D17V6, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  N0               5               128
  N1               2                42
  N2               1                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A
  PCDHGB1 MUTATED     8   0   0
  PCDHGB1 WILD-TYPE 181  31   1
D17V7, multiclass
     clus
vv    PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  M0                8               181
  M1                0                31
  M1A               0                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  PCDHGB1 MUTATED     5   3
  PCDHGB1 WILD-TYPE 102 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB1 MUTATED      5    3
  PCDHGB1 WILD-TYPE  102  113
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  FEMALE               5               102
  MALE                 3               113
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGB1 MUTATED                      5                             2
  PCDHGB1 WILD-TYPE                  125                            20
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGB1 MUTATED                       1                              0
  PCDHGB1 WILD-TYPE                    56                              8
D17V9, multiclass
                                clus
vv                               PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  COLON ADENOCARCINOMA                         5               125
  COLON MUCINOUS ADENOCARCINOMA                2                20
  RECTAL ADENOCARCINOMA                        1                56
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGB1 MUTATED     7   0   0   0
  PCDHGB1 WILD-TYPE 180   2  27   1
D17V10, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  R0               7               180
  R1               0                 2
  R2               0                27
  RX               0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous

Clustering(18) Variable = PCBP1 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  PCBP1 MUTATED     4   0
  PCBP1 WILD-TYPE 165  35
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             200 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              35 
$`PCBP1 MUTATED`
TCGA-AA-3941 TCGA-AA-3979 TCGA-AA-A01I TCGA-AG-3894 
       24.00        24.00        31.00        14.01 

$`PCBP1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
          14.01            0.92 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          31.00          117.11 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          24.00           19.99 
[1] "14.0 - 31.0 (24.0)" "0.9 - 117.1 (20.0)"
[1] "hr="     "9200000"
D18V2, continuous
D18V3, binary
                 cls
clus                0   1
  PCBP1 MUTATED     4   1
  PCBP1 WILD-TYPE 149  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      4    1
  PCBP1 WILD-TYPE  149   67
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON              4             149
  RECTUM             1              67
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCBP1 MUTATED         1        0         3         0         0          0
  PCBP1 WILD-TYPE      48       20        54         4        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED            0          0        0         1
  PCBP1 WILD-TYPE         20         20       31         0
D18V4, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                1              48
  STAGE II               0              20
  STAGE IIA              3              54
  STAGE IIB              0               4
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             0              20
  STAGE IV               0              31
  STAGE IVA              1               0
[1] 10  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
  PCBP1 MUTATED     0   1   3   1
  PCBP1 WILD-TYPE   9  46 146  17
D18V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               9
  T2             1              46
  T3             3             146
  T4             1              17
[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
  PCBP1 MUTATED     4   1   0
  PCBP1 WILD-TYPE 129  43  46
D18V6, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0             4             129
  N1             1              43
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  PCBP1 MUTATED     4   0   1
  PCBP1 WILD-TYPE 185  31   0
D18V7, multiclass
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  M0              4             185
  M1              0              31
  M1A             1               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     2   3
  PCBP1 WILD-TYPE 105 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      2    3
  PCBP1 WILD-TYPE  105  113
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             2             105
  MALE               3             113
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCBP1 MUTATED                      4                             0
  PCBP1 WILD-TYPE                  126                            22
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCBP1 MUTATED                       1                              0
  PCBP1 WILD-TYPE                    56                              8
D18V9, multiclass
                                clus
vv                               PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             126
  COLON MUCINOUS ADENOCARCINOMA              0              22
  RECTAL ADENOCARCINOMA                      1              56
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     5   0   0   0
  PCBP1 WILD-TYPE 182   2  27   1
D18V10, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             5             182
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous

Clustering(19) Variable = ZHX2 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  ZHX2 MUTATED     9   0
  ZHX2 WILD-TYPE 160  35
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             9            195 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             0             35 
$`ZHX2 MUTATED`
TCGA-A6-2672 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00R 
       46.65        26.01        25.02        24.00        38.04         0.99 
TCGA-AA-A010 TCGA-AG-3605 TCGA-AG-3883 
       34.98         0.99         1.02 

$`ZHX2 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        23.38        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       16.31         0.95        17.95        43.04        13.55        12.72 
TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99         7.99         0.99         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  ZHX2 MUTATED ZHX2 WILD-TYPE 
          0.99           0.92 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         46.65         117.11 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         25.02          19.99 
[1] "1.0 - 46.6 (25.0)"  "0.9 - 117.1 (20.0)"
[1] "hr="     "2.6e+07"
D19V2, continuous
D19V3, binary
                cls
clus               0   1
  ZHX2 MUTATED     8   2
  ZHX2 WILD-TYPE 145  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      8    2
  ZHX2 WILD-TYPE  145   66
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON             8            145
  RECTUM            2             66
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ZHX2 MUTATED         2        1         2         1         0          1
  ZHX2 WILD-TYPE      47       19        55         3        18          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX2 MUTATED            1          0        1         0
  ZHX2 WILD-TYPE         19         20       30         1
D19V4, multiclass
            clus
vv           ZHX2 MUTATED ZHX2 WILD-TYPE
  STAGE I               2             47
  STAGE II              1             19
  STAGE IIA             2             55
  STAGE IIB             1              3
  STAGE III             0             18
  STAGE IIIA            1              1
  STAGE IIIB            1             19
  STAGE IIIC            0             20
  STAGE IV              1             30
  STAGE IVA             0              1
[1] 10  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
  ZHX2 MUTATED     0   4   4   2
  ZHX2 WILD-TYPE   9  43 145  16
D19V5, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  T1            0              9
  T2            4             43
  T3            4            145
  T4            2             16
[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
  ZHX2 MUTATED     7   3   0
  ZHX2 WILD-TYPE 126  41  46
D19V6, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  N0            7            126
  N1            3             41
  N2            0             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  ZHX2 MUTATED     8   1   0
  ZHX2 WILD-TYPE 181  30   1
D19V7, multiclass
     clus
vv    ZHX2 MUTATED ZHX2 WILD-TYPE
  M0             8            181
  M1             1             30
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                cls
clus               0   1
  ZHX2 MUTATED     5   5
  ZHX2 WILD-TYPE 102 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      5    5
  ZHX2 WILD-TYPE  102  111
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  FEMALE            5            102
  MALE              5            111
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZHX2 MUTATED                      8                             0
  ZHX2 WILD-TYPE                  122                            22
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZHX2 MUTATED                       2                              0
  ZHX2 WILD-TYPE                    55                              8
D19V9, multiclass
                                clus
vv                               ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            122
  COLON MUCINOUS ADENOCARCINOMA             0             22
  RECTAL ADENOCARCINOMA                     2             55
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZHX2 MUTATED     8   0   1   0
  ZHX2 WILD-TYPE 179   2  26   1
D19V10, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  R0            8            179
  R1            0              2
  R2            1             26
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous

Clustering(20) Variable = PCDHA3 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  PCDHA3 MUTATED     7   5
  PCDHA3 WILD-TYPE 162  30
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
              12              192 
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
               5               30 
$`PCDHA3 MUTATED`
TCGA-A6-2676 TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 
       23.38         0.92         5.03        53.00        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01T TCGA-AY-4070 TCGA-AG-A02G TCGA-AG-A02N 
        4.01        34.98        33.04        16.31        38.96        61.97 

$`PCDHA3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4071 TCGA-AF-2689 
       41.00        39.98        18.05        40.96         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       10.98        49.97         1.94        41.00        38.04       117.11 

  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
            0.92             0.92 
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
           61.97           117.11 
  PCDHA3 MUTATED PCDHA3 WILD-TYPE 
          29.015           19.990 
[1] "0.9 - 62.0 (29.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "2.4"
D20V2, continuous
D20V3, binary
                  cls
clus                 0   1
  PCDHA3 MUTATED    10   2
  PCDHA3 WILD-TYPE 143  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA3 MUTATED     10    2
  PCDHA3 WILD-TYPE  143   66
        clus
vv       PCDHA3 MUTATED PCDHA3 WILD-TYPE
  COLON              10              143
  RECTUM              2               66
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHA3 MUTATED         0        2         0         4         2          0
  PCDHA3 WILD-TYPE      49       18        57         0        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHA3 MUTATED            0          1        2         0
  PCDHA3 WILD-TYPE         20         19       29         1
D20V4, multiclass
            clus
vv           PCDHA3 MUTATED PCDHA3 WILD-TYPE
  STAGE I                 0               49
  STAGE II                2               18
  STAGE IIA               0               57
  STAGE IIB               4                0
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              0               20
  STAGE IIIC              1               19
  STAGE IV                2               29
  STAGE IVA               0                1
[1] 10  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
  PCDHA3 MUTATED     0   2   6   4
  PCDHA3 WILD-TYPE   9  45 143  14
D20V5, multiclass
    clus
vv   PCDHA3 MUTATED PCDHA3 WILD-TYPE
  T1              0                9
  T2              2               45
  T3              6              143
  T4              4               14
[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
  PCDHA3 MUTATED     7   4   1
  PCDHA3 WILD-TYPE 126  40  45
D20V6, multiclass
    clus
vv   PCDHA3 MUTATED PCDHA3 WILD-TYPE
  N0              7              126
  N1              4               40
  N2              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  PCDHA3 MUTATED     9   2   0
  PCDHA3 WILD-TYPE 180  29   1
D20V7, multiclass
     clus
vv    PCDHA3 MUTATED PCDHA3 WILD-TYPE
  M0               9              180
  M1               2               29
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                  cls
clus                 0   1
  PCDHA3 MUTATED     7   5
  PCDHA3 WILD-TYPE 100 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA3 MUTATED      7    5
  PCDHA3 WILD-TYPE  100  111
        clus
vv       PCDHA3 MUTATED PCDHA3 WILD-TYPE
  FEMALE              7              100
  MALE                5              111
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHA3 MUTATED                      8                             2
  PCDHA3 WILD-TYPE                  122                            20
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHA3 MUTATED                       2                              0
  PCDHA3 WILD-TYPE                    55                              8
D20V9, multiclass
                                clus
vv                               PCDHA3 MUTATED PCDHA3 WILD-TYPE
  COLON ADENOCARCINOMA                        8              122
  COLON MUCINOUS ADENOCARCINOMA               2               20
  RECTAL ADENOCARCINOMA                       2               55
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDHA3 MUTATED     8   1   2   0
  PCDHA3 WILD-TYPE 179   1  25   1
D20V10, multiclass
    clus
vv   PCDHA3 MUTATED PCDHA3 WILD-TYPE
  R0              8              179
  R1              1                1
  R2              2               25
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous

Clustering(21) Variable = PCDHA2 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  PCDHA2 MUTATED     8   2
  PCDHA2 WILD-TYPE 161  33
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
              10              194 
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
               2               33 
$`PCDHA2 MUTATED`
TCGA-AA-3666 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3875 TCGA-AA-3966 TCGA-AA-3994 
        2.01         0.99         1.02        18.05         2.01        27.02 
TCGA-AA-A010 TCGA-AG-3892 TCGA-AG-3909 TCGA-AG-A02N 
       34.98        13.02        19.99        61.97 

$`PCDHA2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       13.94        19.99        54.02        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       16.31         0.95        17.95        43.04        13.55        12.72 
TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 
       19.99        19.99         7.99         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
            0.99             0.92 
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
           61.97           117.11 
  PCDHA2 MUTATED PCDHA2 WILD-TYPE 
          15.535           20.980 
[1] "1.0 - 62.0 (15.5)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.5"
D21V2, continuous
D21V3, binary
                  cls
clus                 0   1
  PCDHA2 MUTATED     8   4
  PCDHA2 WILD-TYPE 145  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA2 MUTATED      8    4
  PCDHA2 WILD-TYPE  145   64
        clus
vv       PCDHA2 MUTATED PCDHA2 WILD-TYPE
  COLON               8              145
  RECTUM              4               64
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHA2 MUTATED         3        1         2         1         2          0
  PCDHA2 WILD-TYPE      46       19        55         3        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHA2 MUTATED            3          0        0         0
  PCDHA2 WILD-TYPE         17         20       31         1
D21V4, multiclass
            clus
vv           PCDHA2 MUTATED PCDHA2 WILD-TYPE
  STAGE I                 3               46
  STAGE II                1               19
  STAGE IIA               2               55
  STAGE IIB               1                3
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              3               17
  STAGE IIIC              0               20
  STAGE IV                0               31
  STAGE IVA               0                1
[1] 10  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
  PCDHA2 MUTATED     2   1   7   2
  PCDHA2 WILD-TYPE   7  46 142  16
D21V5, multiclass
    clus
vv   PCDHA2 MUTATED PCDHA2 WILD-TYPE
  T1              2                7
  T2              1               46
  T3              7              142
  T4              2               16
[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
  PCDHA2 MUTATED     7   4   1
  PCDHA2 WILD-TYPE 126  40  45
D21V6, multiclass
    clus
vv   PCDHA2 MUTATED PCDHA2 WILD-TYPE
  N0              7              126
  N1              4               40
  N2              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  PCDHA2 MUTATED    12   0   0
  PCDHA2 WILD-TYPE 177  31   1
D21V7, multiclass
     clus
vv    PCDHA2 MUTATED PCDHA2 WILD-TYPE
  M0              12              177
  M1               0               31
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                  cls
clus                 0   1
  PCDHA2 MUTATED     8   4
  PCDHA2 WILD-TYPE  99 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA2 MUTATED      8    4
  PCDHA2 WILD-TYPE   99  112
        clus
vv       PCDHA2 MUTATED PCDHA2 WILD-TYPE
  FEMALE              8               99
  MALE                4              112
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHA2 MUTATED                      5                             3
  PCDHA2 WILD-TYPE                  125                            19
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHA2 MUTATED                       4                              0
  PCDHA2 WILD-TYPE                    53                              8
D21V9, multiclass
                                clus
vv                               PCDHA2 MUTATED PCDHA2 WILD-TYPE
  COLON ADENOCARCINOMA                        5              125
  COLON MUCINOUS ADENOCARCINOMA               3               19
  RECTAL ADENOCARCINOMA                       4               53
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDHA2 MUTATED    10   0   1   0
  PCDHA2 WILD-TYPE 177   2  26   1
D21V10, multiclass
    clus
vv   PCDHA2 MUTATED PCDHA2 WILD-TYPE
  R0             10              177
  R1              0                2
  R2              1               26
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous

Clustering(22) Variable = ELF3 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED     6   1
  ELF3 WILD-TYPE 163  34
  ELF3 MUTATED ELF3 WILD-TYPE 
             7            197 
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             34 
$`ELF3 MUTATED`
TCGA-A6-2678 TCGA-AA-3979 TCGA-AA-A01V TCGA-AA-A02J TCGA-AG-3599 TCGA-AG-3892 
       42.28        24.00        35.01         5.03        12.03        13.02 
TCGA-AG-3902 
       32.02 

$`ELF3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        23.38        17.79        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02W 
       39.06        51.98        39.98         2.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  ELF3 MUTATED ELF3 WILD-TYPE 
          5.03           0.92 
  ELF3 MUTATED ELF3 WILD-TYPE 
         42.28         117.11 
  ELF3 MUTATED ELF3 WILD-TYPE 
         24.00          19.99 
[1] "5.0 - 42.3 (24.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                cls
clus               0   1
  ELF3 MUTATED     5   3
  ELF3 WILD-TYPE 148  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      5    3
  ELF3 WILD-TYPE  148   65
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  COLON             5            148
  RECTUM            3             65
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ELF3 MUTATED         3        0         2         0         0          0
  ELF3 WILD-TYPE      46       20        55         4        18          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELF3 MUTATED            1          0        2         0
  ELF3 WILD-TYPE         19         20       29         1
D22V4, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               3             46
  STAGE II              0             20
  STAGE IIA             2             55
  STAGE IIB             0              4
  STAGE III             0             18
  STAGE IIIA            0              2
  STAGE IIIB            1             19
  STAGE IIIC            0             20
  STAGE IV              2             29
  STAGE IVA             0              1
[1] 10  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
  ELF3 MUTATED     1   2   4   1
  ELF3 WILD-TYPE   8  45 145  17
D22V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  T1            1              8
  T2            2             45
  T3            4            145
  T4            1             17
[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
  ELF3 MUTATED     6   1   1
  ELF3 WILD-TYPE 127  43  45
D22V6, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            6            127
  N1            1             43
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  ELF3 MUTATED     6   2   0
  ELF3 WILD-TYPE 183  29   1
D22V7, multiclass
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  M0             6            183
  M1             2             29
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                cls
clus               0   1
  ELF3 MUTATED     3   5
  ELF3 WILD-TYPE 104 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      3    5
  ELF3 WILD-TYPE  104  111
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            3            104
  MALE              5            111
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ELF3 MUTATED                      5                             0
  ELF3 WILD-TYPE                  125                            22
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ELF3 MUTATED                       2                              0
  ELF3 WILD-TYPE                    55                              8
D22V9, multiclass
                                clus
vv                               ELF3 MUTATED ELF3 WILD-TYPE
  COLON ADENOCARCINOMA                      5            125
  COLON MUCINOUS ADENOCARCINOMA             0             22
  RECTAL ADENOCARCINOMA                     2             55
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ELF3 MUTATED     6   0   2   0
  ELF3 WILD-TYPE 181   2  25   1
D22V10, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  R0            6            181
  R1            0              2
  R2            2             25
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous

Clustering(23) Variable = CRTC1 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  CRTC1 MUTATED     4   0
  CRTC1 WILD-TYPE 165  35
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              4             200 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              0              35 
$`CRTC1 MUTATED`
TCGA-AA-3667 TCGA-AA-3956 TCGA-AA-3971 TCGA-AG-A025 
       14.01        34.03        16.08        49.97 

$`CRTC1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 
       13.94        19.99        54.02         2.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  CRTC1 MUTATED CRTC1 WILD-TYPE 
          14.01            0.92 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          49.97          117.11 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
         25.055          20.485 
[1] "14.0 - 50.0 (25.1)" "0.9 - 117.1 (20.5)"
[1] "hr="     "9200000"
D23V2, continuous
D23V3, binary
                 cls
clus                0   1
  CRTC1 MUTATED     3   1
  CRTC1 WILD-TYPE 150  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      3    1
  CRTC1 WILD-TYPE  150   67
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON              3             150
  RECTUM             1              67
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CRTC1 MUTATED         2        0         1         0         1          0
  CRTC1 WILD-TYPE      47       20        56         4        17          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRTC1 MUTATED            0          0        0         0
  CRTC1 WILD-TYPE         20         20       31         1
D23V4, multiclass
            clus
vv           CRTC1 MUTATED CRTC1 WILD-TYPE
  STAGE I                2              47
  STAGE II               0              20
  STAGE IIA              1              56
  STAGE IIB              0               4
  STAGE III              1              17
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             0              20
  STAGE IV               0              31
  STAGE IVA              0               1
[1] 10  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
  CRTC1 MUTATED     1   1   2   0
  CRTC1 WILD-TYPE   8  46 147  18
D23V5, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  T1             1               8
  T2             1              46
  T3             2             147
  T4             0              18
[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
  CRTC1 MUTATED     3   1   0
  CRTC1 WILD-TYPE 130  43  46
D23V6, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  N0             3             130
  N1             1              43
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  CRTC1 MUTATED     4   0   0
  CRTC1 WILD-TYPE 185  31   1
D23V7, multiclass
     clus
vv    CRTC1 MUTATED CRTC1 WILD-TYPE
  M0              4             185
  M1              0              31
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                 cls
clus                0   1
  CRTC1 MUTATED     2   2
  CRTC1 WILD-TYPE 105 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      2    2
  CRTC1 WILD-TYPE  105  114
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  FEMALE             2             105
  MALE               2             114
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CRTC1 MUTATED                      3                             0
  CRTC1 WILD-TYPE                  127                            22
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CRTC1 MUTATED                       1                              0
  CRTC1 WILD-TYPE                    56                              8
D23V9, multiclass
                                clus
vv                               CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             127
  COLON MUCINOUS ADENOCARCINOMA              0              22
  RECTAL ADENOCARCINOMA                      1              56
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CRTC1 MUTATED     4   0   0   0
  CRTC1 WILD-TYPE 183   2  27   1
D23V10, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  R0             4             183
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous

Clustering(24) Variable = CASP8 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     8   1
  CASP8 WILD-TYPE 161  34
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             195 
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              34 
$`CASP8 MUTATED`
TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 
        1.02         0.99        26.99         0.99        53.00        33.01 
TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00R 
       38.04        18.05         0.99 

$`CASP8 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.99            0.92 
  CASP8 MUTATED CASP8 WILD-TYPE 
          53.00          117.11 
  CASP8 MUTATED CASP8 WILD-TYPE 
          18.05           20.98 
[1] "1.0 - 53.0 (18.1)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.3"
D24V2, continuous
D24V3, binary
                 cls
clus                0   1
  CASP8 MUTATED    10   0
  CASP8 WILD-TYPE 143  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     10    0
  CASP8 WILD-TYPE  143   68
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  COLON             10             143
  RECTUM             0              68
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CASP8 MUTATED         2        3         3         1         0          0
  CASP8 WILD-TYPE      47       17        54         3        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED            1          0        0         0
  CASP8 WILD-TYPE         19         20       31         1
D24V4, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                2              47
  STAGE II               3              17
  STAGE IIA              3              54
  STAGE IIB              1               3
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             1              19
  STAGE IIIC             0              20
  STAGE IV               0              31
  STAGE IVA              0               1
[1] 10  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     0   2   5   3
  CASP8 WILD-TYPE   9  45 144  15
D24V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             0               9
  T2             2              45
  T3             5             144
  T4             3              15
[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
  CASP8 MUTATED     9   1   0
  CASP8 WILD-TYPE 124  43  46
D24V6, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             9             124
  N1             1              43
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  CASP8 MUTATED    10   0   0
  CASP8 WILD-TYPE 179  31   1
D24V7, multiclass
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  M0             10             179
  M1              0              31
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     5   5
  CASP8 WILD-TYPE 102 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    5
  CASP8 WILD-TYPE  102  111
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             5             102
  MALE               5             111
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP8 MUTATED                      7                             3
  CASP8 WILD-TYPE                  123                            19
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP8 MUTATED                       0                              0
  CASP8 WILD-TYPE                    57                              8
D24V9, multiclass
                                clus
vv                               CASP8 MUTATED CASP8 WILD-TYPE
  COLON ADENOCARCINOMA                       7             123
  COLON MUCINOUS ADENOCARCINOMA              3              19
  RECTAL ADENOCARCINOMA                      0              57
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    10   0   0   0
  CASP8 WILD-TYPE 177   2  27   1
D24V10, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            10             177
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous

Clustering(25) Variable = CACNG3 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  CACNG3 MUTATED     7   1
  CACNG3 WILD-TYPE 162  34
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              196 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               1               34 
$`CACNG3 MUTATED`
TCGA-A6-3808 TCGA-AA-3672 TCGA-AA-3833 TCGA-AA-A010 TCGA-AA-A01D TCGA-AG-3892 
       33.34         0.92        15.95        34.98         0.99        13.02 
TCGA-AG-3894 TCGA-AG-A002 
       14.01        20.98 

$`CACNG3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       34.65        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 
       18.05        40.96        16.31         0.95        17.95        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       13.55        12.72        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  CACNG3 MUTATED CACNG3 WILD-TYPE 
            0.92             0.92 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
           34.98           117.11 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
           14.98            20.98 
[1] "0.9 - 35.0 (15.0)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     5   3
  CACNG3 WILD-TYPE 148  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      5    3
  CACNG3 WILD-TYPE  148   65
        clus
vv       CACNG3 MUTATED CACNG3 WILD-TYPE
  COLON               5              148
  RECTUM              3               65
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CACNG3 MUTATED         2        0         3         1         1          0
  CACNG3 WILD-TYPE      47       20        54         3        17          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CACNG3 MUTATED            0          1        0         0
  CACNG3 WILD-TYPE         20         19       31         1
D25V4, multiclass
            clus
vv           CACNG3 MUTATED CACNG3 WILD-TYPE
  STAGE I                 2               47
  STAGE II                0               20
  STAGE IIA               3               54
  STAGE IIB               1                3
  STAGE III               1               17
  STAGE IIIA              0                2
  STAGE IIIB              0               20
  STAGE IIIC              1               19
  STAGE IV                0               31
  STAGE IVA               0                1
[1] 10  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
  CACNG3 MUTATED     1   1   5   1
  CACNG3 WILD-TYPE   8  46 144  17
D25V5, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  T1              1                8
  T2              1               46
  T3              5              144
  T4              1               17
[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
  CACNG3 MUTATED     6   1   1
  CACNG3 WILD-TYPE 127  43  45
D25V6, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  N0              6              127
  N1              1               43
  N2              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  CACNG3 MUTATED     8   0   0
  CACNG3 WILD-TYPE 181  31   1
D25V7, multiclass
     clus
vv    CACNG3 MUTATED CACNG3 WILD-TYPE
  M0               8              181
  M1               0               31
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     5   3
  CACNG3 WILD-TYPE 102 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      5    3
  CACNG3 WILD-TYPE  102  113
        clus
vv       CACNG3 MUTATED CACNG3 WILD-TYPE
  FEMALE              5              102
  MALE                3              113
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CACNG3 MUTATED                      4                             1
  CACNG3 WILD-TYPE                  126                            21
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CACNG3 MUTATED                       3                              0
  CACNG3 WILD-TYPE                    54                              8
D25V9, multiclass
                                clus
vv                               CACNG3 MUTATED CACNG3 WILD-TYPE
  COLON ADENOCARCINOMA                        4              126
  COLON MUCINOUS ADENOCARCINOMA               1               21
  RECTAL ADENOCARCINOMA                       3               54
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CACNG3 MUTATED     8   0   0   0
  CACNG3 WILD-TYPE 179   2  27   1
D25V10, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  R0              8              179
  R1              0                2
  R2              0               27
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous

Clustering(26) Variable = PCDHGA7 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  PCDHGA7 MUTATED     3   1
  PCDHGA7 WILD-TYPE 166  34
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                4               200 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                1                34 
$`PCDHGA7 MUTATED`
TCGA-AA-3678 TCGA-AA-3949 TCGA-AA-3979 TCGA-AA-A00N 
       47.01        26.01        24.00         4.01 

$`PCDHGA7 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        33.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
             4.01              0.92 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
            47.01            117.11 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
           25.005            19.990 
[1] "4.0 - 47.0 (25.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.2"
D26V2, continuous
D26V3, binary
                   cls
clus                  0   1
  PCDHGA7 MUTATED     5   0
  PCDHGA7 WILD-TYPE 148  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA7 MUTATED      5    0
  PCDHGA7 WILD-TYPE  148   68
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  COLON                5               148
  RECTUM               0                68
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHGA7 MUTATED         0        0         2         1         1          0
  PCDHGA7 WILD-TYPE      49       20        55         3        17          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGA7 MUTATED            1          0        0         0
  PCDHGA7 WILD-TYPE         19         20       31         1
D26V4, multiclass
            clus
vv           PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  STAGE I                  0                49
  STAGE II                 0                20
  STAGE IIA                2                55
  STAGE IIB                1                 3
  STAGE III                1                17
  STAGE IIIA               0                 2
  STAGE IIIB               1                19
  STAGE IIIC               0                20
  STAGE IV                 0                31
  STAGE IVA                0                 1
[1] 10  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
  PCDHGA7 MUTATED     0   1   3   1
  PCDHGA7 WILD-TYPE   9  46 146  17
D26V5, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  T1               0                 9
  T2               1                46
  T3               3               146
  T4               1                17
[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
  PCDHGA7 MUTATED     3   2   0
  PCDHGA7 WILD-TYPE 130  42  46
D26V6, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  N0               3               130
  N1               2                42
  N2               0                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A
  PCDHGA7 MUTATED     5   0   0
  PCDHGA7 WILD-TYPE 184  31   1
D26V7, multiclass
     clus
vv    PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  M0                5               184
  M1                0                31
  M1A               0                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                   cls
clus                  0   1
  PCDHGA7 MUTATED     3   2
  PCDHGA7 WILD-TYPE 104 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA7 MUTATED      3    2
  PCDHGA7 WILD-TYPE  104  114
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  FEMALE               3               104
  MALE                 2               114
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGA7 MUTATED                      3                             2
  PCDHGA7 WILD-TYPE                  127                            20
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGA7 MUTATED                       0                              0
  PCDHGA7 WILD-TYPE                    57                              8
D26V9, multiclass
                                clus
vv                               PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  COLON ADENOCARCINOMA                         3               127
  COLON MUCINOUS ADENOCARCINOMA                2                20
  RECTAL ADENOCARCINOMA                        0                57
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGA7 MUTATED     5   0   0   0
  PCDHGA7 WILD-TYPE 182   2  27   1
D26V10, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  R0               5               182
  R1               0                 2
  R2               0                27
  RX               0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous

Clustering(27) Variable = CCBP2 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  CCBP2 MUTATED     8   0
  CCBP2 WILD-TYPE 161  35
  CCBP2 MUTATED CCBP2 WILD-TYPE 
              8             196 
  CCBP2 MUTATED CCBP2 WILD-TYPE 
              0              35 
$`CCBP2 MUTATED`
TCGA-AA-3543 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3972 TCGA-AG-3892 TCGA-AG-A002 
        0.99        47.01        26.99        50.99        13.02        20.98 
TCGA-AG-A008 TCGA-AG-A00H 
       13.94        25.97 

$`CCBP2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  CCBP2 MUTATED CCBP2 WILD-TYPE 
           0.99            0.92 
  CCBP2 MUTATED CCBP2 WILD-TYPE 
          50.99          117.11 
  CCBP2 MUTATED CCBP2 WILD-TYPE 
         23.475          19.990 
[1] "1.0 - 51.0 (23.5)"  "0.9 - 117.1 (20.0)"
[1] "hr="     "2.6e+07"
D27V2, continuous
D27V3, binary
                 cls
clus                0   1
  CCBP2 MUTATED     5   5
  CCBP2 WILD-TYPE 148  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCBP2 MUTATED      5    5
  CCBP2 WILD-TYPE  148   63
        clus
vv       CCBP2 MUTATED CCBP2 WILD-TYPE
  COLON              5             148
  RECTUM             5              63
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CCBP2 MUTATED         4        0         4         0         1          0
  CCBP2 WILD-TYPE      45       20        53         4        17          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCBP2 MUTATED            0          0        1         0
  CCBP2 WILD-TYPE         20         20       30         1
D27V4, multiclass
            clus
vv           CCBP2 MUTATED CCBP2 WILD-TYPE
  STAGE I                4              45
  STAGE II               0              20
  STAGE IIA              4              53
  STAGE IIB              0               4
  STAGE III              1              17
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             0              20
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  CCBP2 MUTATED     1   4   5   0
  CCBP2 WILD-TYPE   8  43 144  18
D27V5, multiclass
    clus
vv   CCBP2 MUTATED CCBP2 WILD-TYPE
  T1             1               8
  T2             4              43
  T3             5             144
  T4             0              18
[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
  CCBP2 MUTATED     8   2   0
  CCBP2 WILD-TYPE 125  42  46
D27V6, multiclass
    clus
vv   CCBP2 MUTATED CCBP2 WILD-TYPE
  N0             8             125
  N1             2              42
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  CCBP2 MUTATED     9   1   0
  CCBP2 WILD-TYPE 180  30   1
D27V7, multiclass
     clus
vv    CCBP2 MUTATED CCBP2 WILD-TYPE
  M0              9             180
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                 cls
clus                0   1
  CCBP2 MUTATED     6   4
  CCBP2 WILD-TYPE 101 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCBP2 MUTATED      6    4
  CCBP2 WILD-TYPE  101  112
        clus
vv       CCBP2 MUTATED CCBP2 WILD-TYPE
  FEMALE             6             101
  MALE               4             112
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCBP2 MUTATED                      4                             1
  CCBP2 WILD-TYPE                  126                            21
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCBP2 MUTATED                       4                              1
  CCBP2 WILD-TYPE                    53                              7
D27V9, multiclass
                                clus
vv                               CCBP2 MUTATED CCBP2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             126
  COLON MUCINOUS ADENOCARCINOMA              1              21
  RECTAL ADENOCARCINOMA                      4              53
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCBP2 MUTATED     9   0   1   0
  CCBP2 WILD-TYPE 178   2  26   1
D27V10, multiclass
    clus
vv   CCBP2 MUTATED CCBP2 WILD-TYPE
  R0             9             178
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous

Clustering(28) Variable = MAP2K4 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  MAP2K4 MUTATED     7   2
  MAP2K4 WILD-TYPE 162  33
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               9              195 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               2               33 
$`MAP2K4 MUTATED`
TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A00N 
        0.92        53.00         2.01         2.01        19.07         4.01 
TCGA-AA-A010 TCGA-AG-3727 TCGA-AG-A00Y 
       34.98         0.99        23.01 

$`MAP2K4 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        19.99        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       16.31         0.95        17.95        43.04        13.55        12.72 
TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       19.99        19.99         7.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
            0.92             0.92 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
           53.00           117.11 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
            4.01            20.98 
[1] "0.9 - 53.0 (4.0)"   "0.9 - 117.1 (21.0)"
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED     9   2
  MAP2K4 WILD-TYPE 144  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED      9    2
  MAP2K4 WILD-TYPE  144   66
        clus
vv       MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON               9              144
  RECTUM              2               66
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MAP2K4 MUTATED         1        1         4         2         2          0
  MAP2K4 WILD-TYPE      48       19        53         2        16          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP2K4 MUTATED            0          1        0         0
  MAP2K4 WILD-TYPE         20         19       31         1
D28V4, multiclass
            clus
vv           MAP2K4 MUTATED MAP2K4 WILD-TYPE
  STAGE I                 1               48
  STAGE II                1               19
  STAGE IIA               4               53
  STAGE IIB               2                2
  STAGE III               2               16
  STAGE IIIA              0                2
  STAGE IIIB              0               20
  STAGE IIIC              1               19
  STAGE IV                0               31
  STAGE IVA               0                1
[1] 10  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
  MAP2K4 MUTATED     0   1   8   2
  MAP2K4 WILD-TYPE   9  46 141  16
D28V5, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  T1              0                9
  T2              1               46
  T3              8              141
  T4              2               16
[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
  MAP2K4 MUTATED     8   2   1
  MAP2K4 WILD-TYPE 125  42  45
D28V6, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  N0              8              125
  N1              2               42
  N2              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  MAP2K4 MUTATED    11   0   0
  MAP2K4 WILD-TYPE 178  31   1
D28V7, multiclass
     clus
vv    MAP2K4 MUTATED MAP2K4 WILD-TYPE
  M0              11              178
  M1               0               31
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED     6   5
  MAP2K4 WILD-TYPE 101 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED      6    5
  MAP2K4 WILD-TYPE  101  111
        clus
vv       MAP2K4 MUTATED MAP2K4 WILD-TYPE
  FEMALE              6              101
  MALE                5              111
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP2K4 MUTATED                      7                             2
  MAP2K4 WILD-TYPE                  123                            20
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP2K4 MUTATED                       2                              0
  MAP2K4 WILD-TYPE                    55                              8
D28V9, multiclass
                                clus
vv                               MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON ADENOCARCINOMA                        7              123
  COLON MUCINOUS ADENOCARCINOMA               2               20
  RECTAL ADENOCARCINOMA                       2               55
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP2K4 MUTATED    10   0   0   0
  MAP2K4 WILD-TYPE 177   2  27   1
D28V10, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  R0             10              177
  R1              0                2
  R2              0               27
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous

Clustering(29) Variable = PCDHGA9 MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                 0   1
  PCDHGA9 MUTATED     5   1
  PCDHGA9 WILD-TYPE 164  34
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                6               198 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                1                34 
$`PCDHGA9 MUTATED`
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3877 TCGA-AY-4070 TCGA-AG-A02X 
       54.02         0.92        53.00        31.00        16.31        41.00 

$`PCDHGA9 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       13.94        19.99         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 
       39.98        18.05        40.96         0.95        17.95        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       13.55        12.72        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        61.97        38.04       117.11 

  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
             0.92              0.92 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
            54.02            117.11 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
            36.00             19.99 
[1] "0.9 - 54.0 (36.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.4"
D29V2, continuous
D29V3, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     5   1
  PCDHGA9 WILD-TYPE 148  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      5    1
  PCDHGA9 WILD-TYPE  148   67
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  COLON                5               148
  RECTUM               1                67
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHGA9 MUTATED         2        2         0         0         1          0
  PCDHGA9 WILD-TYPE      47       18        57         4        17          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGA9 MUTATED            0          1        0         0
  PCDHGA9 WILD-TYPE         20         19       31         1
D29V4, multiclass
            clus
vv           PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  STAGE I                  2                47
  STAGE II                 2                18
  STAGE IIA                0                57
  STAGE IIB                0                 4
  STAGE III                1                17
  STAGE IIIA               0                 2
  STAGE IIIB               0                20
  STAGE IIIC               1                19
  STAGE IV                 0                31
  STAGE IVA                0                 1
[1] 10  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
  PCDHGA9 MUTATED     1   1   4   0
  PCDHGA9 WILD-TYPE   8  46 145  18
D29V5, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  T1               1                 8
  T2               1                46
  T3               4               145
  T4               0                18
[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
  PCDHGA9 MUTATED     4   1   1
  PCDHGA9 WILD-TYPE 129  43  45
D29V6, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  N0               4               129
  N1               1                43
  N2               1                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A
  PCDHGA9 MUTATED     6   0   0
  PCDHGA9 WILD-TYPE 183  31   1
D29V7, multiclass
     clus
vv    PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  M0                6               183
  M1                0                31
  M1A               0                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     4   2
  PCDHGA9 WILD-TYPE 103 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      4    2
  PCDHGA9 WILD-TYPE  103  114
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  FEMALE               4               103
  MALE                 2               114
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGA9 MUTATED                      4                             1
  PCDHGA9 WILD-TYPE                  126                            21
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGA9 MUTATED                       1                              0
  PCDHGA9 WILD-TYPE                    56                              8
D29V9, multiclass
                                clus
vv                               PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  COLON ADENOCARCINOMA                         4               126
  COLON MUCINOUS ADENOCARCINOMA                1                21
  RECTAL ADENOCARCINOMA                        1                56
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGA9 MUTATED     5   1   0   0
  PCDHGA9 WILD-TYPE 182   1  27   1
D29V10, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  R0               5               182
  R1               1                 1
  R2               0                27
  RX               0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous

Clustering(30) Variable = RBM10 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED     4   3
  RBM10 WILD-TYPE 165  32
  RBM10 MUTATED RBM10 WILD-TYPE 
              7             197 
  RBM10 MUTATED RBM10 WILD-TYPE 
              3              32 
$`RBM10 MUTATED`
TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3941 TCGA-AF-2689 TCGA-AG-3583 TCGA-AG-3902 
        0.92         0.99        24.00        17.95         2.01        32.02 
TCGA-AG-3999 
       28.04 

$`RBM10 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        19.99        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       35.01        14.01         1.02        48.03        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.92            0.92 
  RBM10 MUTATED RBM10 WILD-TYPE 
          32.02          117.11 
  RBM10 MUTATED RBM10 WILD-TYPE 
          17.95           20.98 
[1] "0.9 - 32.0 (17.9)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "4"  
D30V2, continuous
D30V3, binary
                 cls
clus                0   1
  RBM10 MUTATED     4   4
  RBM10 WILD-TYPE 149  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4    4
  RBM10 WILD-TYPE  149   64
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  COLON              4             149
  RECTUM             4              64
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RBM10 MUTATED         0        1         1         0         2          0
  RBM10 WILD-TYPE      49       19        56         4        16          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM10 MUTATED            0          1        2         1
  RBM10 WILD-TYPE         20         19       29         0
D30V4, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0              49
  STAGE II               1              19
  STAGE IIA              1              56
  STAGE IIB              0               4
  STAGE III              2              16
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             1              19
  STAGE IV               2              29
  STAGE IVA              1               0
[1] 10  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
  RBM10 MUTATED     0   0   6   2
  RBM10 WILD-TYPE   9  47 143  16
D30V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             0               9
  T2             0              47
  T3             6             143
  T4             2              16
[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
  RBM10 MUTATED     2   2   4
  RBM10 WILD-TYPE 131  42  42
D30V6, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0             2             131
  N1             2              42
  N2             4              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  RBM10 MUTATED     5   2   1
  RBM10 WILD-TYPE 184  29   0
D30V7, multiclass
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  M0              5             184
  M1              2              29
  M1A             1               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                 cls
clus                0   1
  RBM10 MUTATED     6   2
  RBM10 WILD-TYPE 101 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      6    2
  RBM10 WILD-TYPE  101  114
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             6             101
  MALE               2             114
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM10 MUTATED                      4                             0
  RBM10 WILD-TYPE                  126                            22
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM10 MUTATED                       3                              1
  RBM10 WILD-TYPE                    54                              7
D30V9, multiclass
                                clus
vv                               RBM10 MUTATED RBM10 WILD-TYPE
  COLON ADENOCARCINOMA                       4             126
  COLON MUCINOUS ADENOCARCINOMA              0              22
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM10 MUTATED     7   0   1   0
  RBM10 WILD-TYPE 180   2  26   1
D30V10, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             7             180
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous

Clustering(31) Variable = PTEN MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     5   1
  PTEN WILD-TYPE 164  34
  PTEN MUTATED PTEN WILD-TYPE 
             6            198 
  PTEN MUTATED PTEN WILD-TYPE 
             1             34 
$`PTEN MUTATED`
TCGA-AA-3692 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AG-3892 TCGA-AG-A002 
       36.00        53.00        25.02        34.98        13.02        20.98 

$`PTEN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       19.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 

  PTEN MUTATED PTEN WILD-TYPE 
         13.02           0.92 
  PTEN MUTATED PTEN WILD-TYPE 
         53.00         117.11 
  PTEN MUTATED PTEN WILD-TYPE 
         30.00          19.99 
[1] "13.0 - 53.0 (30.0)" "0.9 - 117.1 (20.0)"
[1] "hr=" "1.3"
D31V2, continuous
D31V3, binary
                cls
clus               0   1
  PTEN MUTATED     4   3
  PTEN WILD-TYPE 149  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE  149   65
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  COLON             4            149
  RECTUM            3             65
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PTEN MUTATED         2        1         0         1         0          0
  PTEN WILD-TYPE      47       19        57         3        18          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED            1          0        1         0
  PTEN WILD-TYPE         19         20       30         1
D31V4, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               2             47
  STAGE II              1             19
  STAGE IIA             0             57
  STAGE IIB             1              3
  STAGE III             0             18
  STAGE IIIA            0              2
  STAGE IIIB            1             19
  STAGE IIIC            0             20
  STAGE IV              1             30
  STAGE IVA             0              1
[1] 10  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
  PTEN MUTATED     1   2   3   1
  PTEN WILD-TYPE   8  45 146  17
D31V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            1              8
  T2            2             45
  T3            3            146
  T4            1             17
[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
  PTEN MUTATED     5   1   1
  PTEN WILD-TYPE 128  43  45
D31V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            5            128
  N1            1             43
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  PTEN MUTATED     5   1   0
  PTEN WILD-TYPE 184  30   1
D31V7, multiclass
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  M0             5            184
  M1             1             30
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                cls
clus               0   1
  PTEN MUTATED     4   3
  PTEN WILD-TYPE 103 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE  103  113
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            103
  MALE              3            113
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTEN MUTATED                      3                             1
  PTEN WILD-TYPE                  127                            21
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTEN MUTATED                       2                              1
  PTEN WILD-TYPE                    55                              7
D31V9, multiclass
                                clus
vv                               PTEN MUTATED PTEN WILD-TYPE
  COLON ADENOCARCINOMA                      3            127
  COLON MUCINOUS ADENOCARCINOMA             1             21
  RECTAL ADENOCARCINOMA                     2             55
  RECTAL MUCINOUS ADENOCARCINOMA            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     5   0   1   0
  PTEN WILD-TYPE 182   2  26   1
D31V10, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            5            182
  R1            0              2
  R2            1             26
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous

Clustering(32) Variable = DNMT1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  DNMT1 MUTATED    13   3
  DNMT1 WILD-TYPE 156  32
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             16             188 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
              3              32 
$`DNMT1 MUTATED`
TCGA-A6-2683 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-3956 TCGA-AA-3966 
       15.52        29.95         0.92        31.00        34.03         2.01 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AF-2689 
       18.05         4.01        34.98         1.02        37.02        17.95 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-A002 TCGA-AG-A02N 
       19.99        19.99        20.98        61.97 

$`DNMT1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-3807 
       46.65        43.76        23.38        17.79        42.28        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       26.01         2.01        20.98        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        17.03        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2691 TCGA-AF-2692 
       18.05        40.96        16.31         0.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3883 
       15.95        19.99         7.99         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  DNMT1 MUTATED DNMT1 WILD-TYPE 
           0.92            0.92 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          61.97          117.11 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          19.99           20.98 
[1] "0.9 - 62.0 (20.0)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                 cls
clus                0   1
  DNMT1 MUTATED    12   5
  DNMT1 WILD-TYPE 141  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     12    5
  DNMT1 WILD-TYPE  141   63
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON             12             141
  RECTUM             5              63
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  DNMT1 MUTATED         3        3         4         2         1          0
  DNMT1 WILD-TYPE      46       17        53         2        17          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNMT1 MUTATED            1          1        2         0
  DNMT1 WILD-TYPE         19         19       29         1
D32V4, multiclass
            clus
vv           DNMT1 MUTATED DNMT1 WILD-TYPE
  STAGE I                3              46
  STAGE II               3              17
  STAGE IIA              4              53
  STAGE IIB              2               2
  STAGE III              1              17
  STAGE IIIA             0               2
  STAGE IIIB             1              19
  STAGE IIIC             1              19
  STAGE IV               2              29
  STAGE IVA              0               1
[1] 10  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
  DNMT1 MUTATED     1   2  10   4
  DNMT1 WILD-TYPE   8  45 139  14
D32V5, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  T1             1               8
  T2             2              45
  T3            10             139
  T4             4              14
[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
  DNMT1 MUTATED    13   2   2
  DNMT1 WILD-TYPE 120  42  44
D32V6, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  N0            13             120
  N1             2              42
  N2             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  DNMT1 MUTATED    15   2   0
  DNMT1 WILD-TYPE 174  29   1
D32V7, multiclass
     clus
vv    DNMT1 MUTATED DNMT1 WILD-TYPE
  M0             15             174
  M1              2              29
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED    11   6
  DNMT1 WILD-TYPE  96 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     11    6
  DNMT1 WILD-TYPE   96  110
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  FEMALE            11              96
  MALE               6             110
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNMT1 MUTATED                      7                             5
  DNMT1 WILD-TYPE                  123                            17
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNMT1 MUTATED                       5                              0
  DNMT1 WILD-TYPE                    52                              8
D32V9, multiclass
                                clus
vv                               DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             123
  COLON MUCINOUS ADENOCARCINOMA              5              17
  RECTAL ADENOCARCINOMA                      5              52
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DNMT1 MUTATED    16   0   0   0
  DNMT1 WILD-TYPE 171   2  27   1
D32V10, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  R0            16             171
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous

Clustering(33) Variable = BCOR MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  BCOR MUTATED     6   2
  BCOR WILD-TYPE 163  33
  BCOR MUTATED BCOR WILD-TYPE 
             8            196 
  BCOR MUTATED BCOR WILD-TYPE 
             2             33 
$`BCOR MUTATED`
TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3930 TCGA-AA-A00N TCGA-AA-A010 TCGA-AG-3605 
       29.95         0.92         2.01         4.01        34.98         0.99 
TCGA-AG-3878 TCGA-AG-3892 
        0.99        13.02 

$`BCOR WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 
       18.05        40.96        16.31         0.95        17.95        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       13.55        12.72        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3882 
       15.95        19.99        19.99         7.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  BCOR MUTATED BCOR WILD-TYPE 
          0.92           0.92 
  BCOR MUTATED BCOR WILD-TYPE 
         34.98         117.11 
  BCOR MUTATED BCOR WILD-TYPE 
          3.01          20.98 
[1] "0.9 - 35.0 (3.0)"   "0.9 - 117.1 (21.0)"
[1] "hr=" "2.9"
D33V2, continuous
D33V3, binary
                cls
clus               0   1
  BCOR MUTATED     6   3
  BCOR WILD-TYPE 147  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      6    3
  BCOR WILD-TYPE  147   65
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  COLON             6            147
  RECTUM            3             65
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BCOR MUTATED         2        1         1         2         1          0
  BCOR WILD-TYPE      47       19        56         2        17          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED            0          0        2         0
  BCOR WILD-TYPE         20         20       29         1
D33V4, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               2             47
  STAGE II              1             19
  STAGE IIA             1             56
  STAGE IIB             2              2
  STAGE III             1             17
  STAGE IIIA            0              2
  STAGE IIIB            0             20
  STAGE IIIC            0             20
  STAGE IV              2             29
  STAGE IVA             0              1
[1] 10  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
  BCOR MUTATED     1   1   4   3
  BCOR WILD-TYPE   8  46 145  15
D33V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            1              8
  T2            1             46
  T3            4            145
  T4            3             15
[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
  BCOR MUTATED     6   2   1
  BCOR WILD-TYPE 127  42  45
D33V6, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0            6            127
  N1            2             42
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  BCOR MUTATED     7   2   0
  BCOR WILD-TYPE 182  29   1
D33V7, multiclass
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  M0             7            182
  M1             2             29
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                cls
clus               0   1
  BCOR MUTATED     6   3
  BCOR WILD-TYPE 101 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      6    3
  BCOR WILD-TYPE  101  113
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE            6            101
  MALE              3            113
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCOR MUTATED                      4                             2
  BCOR WILD-TYPE                  126                            20
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCOR MUTATED                       3                              0
  BCOR WILD-TYPE                    54                              8
D33V9, multiclass
                                clus
vv                               BCOR MUTATED BCOR WILD-TYPE
  COLON ADENOCARCINOMA                      4            126
  COLON MUCINOUS ADENOCARCINOMA             2             20
  RECTAL ADENOCARCINOMA                     3             54
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED     7   0   2   0
  BCOR WILD-TYPE 180   2  25   1
D33V10, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0            7            180
  R1            0              2
  R2            2             25
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous

Clustering(34) Variable = PCDHGB5 MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  PCDHGB5 MUTATED     4   3
  PCDHGB5 WILD-TYPE 165  32
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
                7               197 
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
                3                32 
$`PCDHGB5 MUTATED`
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01I TCGA-AA-A02J 
       53.00        33.01        25.02         4.01        31.00         5.03 
TCGA-AG-A026 
        1.94 

$`PCDHGB5 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
             1.94              0.92 
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
            53.00            117.11 
  PCDHGB5 MUTATED PCDHGB5 WILD-TYPE 
            25.02             19.99 
[1] "1.9 - 53.0 (25.0)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "2.8"
D34V2, continuous
D34V3, binary
                   cls
clus                  0   1
  PCDHGB5 MUTATED     6   1
  PCDHGB5 WILD-TYPE 147  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB5 MUTATED      6    1
  PCDHGB5 WILD-TYPE  147   67
        clus
vv       PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  COLON                6               147
  RECTUM               1                67
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHGB5 MUTATED         1        2         0         2         0          0
  PCDHGB5 WILD-TYPE      48       18        57         2        18          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGB5 MUTATED            0          0        1         0
  PCDHGB5 WILD-TYPE         20         20       30         1
D34V4, multiclass
            clus
vv           PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  STAGE I                  1                48
  STAGE II                 2                18
  STAGE IIA                0                57
  STAGE IIB                2                 2
  STAGE III                0                18
  STAGE IIIA               0                 2
  STAGE IIIB               0                20
  STAGE IIIC               0                20
  STAGE IV                 1                30
  STAGE IVA                0                 1
[1] 10  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
  PCDHGB5 MUTATED     0   2   2   3
  PCDHGB5 WILD-TYPE   9  45 147  15
D34V5, multiclass
    clus
vv   PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  T1               0                 9
  T2               2                45
  T3               2               147
  T4               3                15
[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
  PCDHGB5 MUTATED     7   0   0
  PCDHGB5 WILD-TYPE 126  44  46
D34V6, multiclass
    clus
vv   PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  N0               7               126
  N1               0                44
  N2               0                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A
  PCDHGB5 MUTATED     5   1   0
  PCDHGB5 WILD-TYPE 184  30   1
D34V7, multiclass
     clus
vv    PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  M0                5               184
  M1                1                30
  M1A               0                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                   cls
clus                  0   1
  PCDHGB5 MUTATED     2   5
  PCDHGB5 WILD-TYPE 105 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB5 MUTATED      2    5
  PCDHGB5 WILD-TYPE  105  111
        clus
vv       PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  FEMALE               2               105
  MALE                 5               111
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGB5 MUTATED                      4                             2
  PCDHGB5 WILD-TYPE                  126                            20
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGB5 MUTATED                       1                              0
  PCDHGB5 WILD-TYPE                    56                              8
D34V9, multiclass
                                clus
vv                               PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  COLON ADENOCARCINOMA                         4               126
  COLON MUCINOUS ADENOCARCINOMA                2                20
  RECTAL ADENOCARCINOMA                        1                56
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGB5 MUTATED     4   1   1   0
  PCDHGB5 WILD-TYPE 183   1  26   1
D34V10, multiclass
    clus
vv   PCDHGB5 MUTATED PCDHGB5 WILD-TYPE
  R0               4               183
  R1               1                 1
  R2               1                26
  RX               0                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous

Clustering(35) Variable = ZFP3 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  ZFP3 MUTATED     8   0
  ZFP3 WILD-TYPE 161  35
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             8            196 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             0             35 
$`ZFP3 MUTATED`
TCGA-A6-2672 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A010 
       46.65         8.05        29.95        15.95        25.02        34.98 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`ZFP3 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        23.38        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        37.05        36.03        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       40.96        16.31         0.95        17.95        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  ZFP3 MUTATED ZFP3 WILD-TYPE 
          8.05           0.92 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
         46.65         117.11 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
         23.00          19.99 
[1] "8.1 - 46.6 (23.0)"  "0.9 - 117.1 (20.0)"
[1] "hr="     "2.6e+07"
D35V2, continuous
D35V3, binary
                cls
clus               0   1
  ZFP3 MUTATED     6   2
  ZFP3 WILD-TYPE 147  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      6    2
  ZFP3 WILD-TYPE  147   66
        clus
vv       ZFP3 MUTATED ZFP3 WILD-TYPE
  COLON             6            147
  RECTUM            2             66
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ZFP3 MUTATED         2        0         2         1         0          0
  ZFP3 WILD-TYPE      47       20        55         3        18          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP3 MUTATED            2          0        0         0
  ZFP3 WILD-TYPE         18         20       31         1
D35V4, multiclass
            clus
vv           ZFP3 MUTATED ZFP3 WILD-TYPE
  STAGE I               2             47
  STAGE II              0             20
  STAGE IIA             2             55
  STAGE IIB             1              3
  STAGE III             0             18
  STAGE IIIA            0              2
  STAGE IIIB            2             18
  STAGE IIIC            0             20
  STAGE IV              0             31
  STAGE IVA             0              1
[1] 10  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
  ZFP3 MUTATED     1   2   4   1
  ZFP3 WILD-TYPE   8  45 145  17
D35V5, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  T1            1              8
  T2            2             45
  T3            4            145
  T4            1             17
[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
  ZFP3 MUTATED     6   2   0
  ZFP3 WILD-TYPE 127  42  46
D35V6, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  N0            6            127
  N1            2             42
  N2            0             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  ZFP3 MUTATED     7   0   0
  ZFP3 WILD-TYPE 182  31   1
D35V7, multiclass
     clus
vv    ZFP3 MUTATED ZFP3 WILD-TYPE
  M0             7            182
  M1             0             31
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                cls
clus               0   1
  ZFP3 MUTATED     5   3
  ZFP3 WILD-TYPE 102 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      5    3
  ZFP3 WILD-TYPE  102  113
        clus
vv       ZFP3 MUTATED ZFP3 WILD-TYPE
  FEMALE            5            102
  MALE              3            113
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFP3 MUTATED                      5                             1
  ZFP3 WILD-TYPE                  125                            21
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFP3 MUTATED                       2                              0
  ZFP3 WILD-TYPE                    55                              8
D35V9, multiclass
                                clus
vv                               ZFP3 MUTATED ZFP3 WILD-TYPE
  COLON ADENOCARCINOMA                      5            125
  COLON MUCINOUS ADENOCARCINOMA             1             21
  RECTAL ADENOCARCINOMA                     2             55
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZFP3 MUTATED     7   0   0   0
  ZFP3 WILD-TYPE 180   2  27   1
D35V10, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  R0            7            180
  R1            0              2
  R2            0             27
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous

Clustering(36) Variable = RWDD2B MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  RWDD2B MUTATED     5   1
  RWDD2B WILD-TYPE 164  34
  RWDD2B MUTATED RWDD2B WILD-TYPE 
               6              198 
  RWDD2B MUTATED RWDD2B WILD-TYPE 
               1               34 
$`RWDD2B MUTATED`
TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AG-3726 TCGA-AG-3892 
        0.99        25.02        38.04        34.98         7.99        13.02 

$`RWDD2B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 
        6.05         0.99        15.95        19.99        19.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 

  RWDD2B MUTATED RWDD2B WILD-TYPE 
            0.99             0.92 
  RWDD2B MUTATED RWDD2B WILD-TYPE 
           38.04           117.11 
  RWDD2B MUTATED RWDD2B WILD-TYPE 
          19.020           20.485 
[1] "1.0 - 38.0 (19.0)"  "0.9 - 117.1 (20.5)"
[1] "hr=" "1.2"
D36V2, continuous
D36V3, binary
                  cls
clus                 0   1
  RWDD2B MUTATED     5   2
  RWDD2B WILD-TYPE 148  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD2B MUTATED      5    2
  RWDD2B WILD-TYPE  148   66
        clus
vv       RWDD2B MUTATED RWDD2B WILD-TYPE
  COLON               5              148
  RECTUM              2               66
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RWDD2B MUTATED         2        1         2         1         0          0
  RWDD2B WILD-TYPE      47       19        55         3        18          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RWDD2B MUTATED            0          0        0         0
  RWDD2B WILD-TYPE         20         20       31         1
D36V4, multiclass
            clus
vv           RWDD2B MUTATED RWDD2B WILD-TYPE
  STAGE I                 2               47
  STAGE II                1               19
  STAGE IIA               2               55
  STAGE IIB               1                3
  STAGE III               0               18
  STAGE IIIA              0                2
  STAGE IIIB              0               20
  STAGE IIIC              0               20
  STAGE IV                0               31
  STAGE IVA               0                1
[1] 10  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
  RWDD2B MUTATED     1   2   3   1
  RWDD2B WILD-TYPE   8  45 146  17
D36V5, multiclass
    clus
vv   RWDD2B MUTATED RWDD2B WILD-TYPE
  T1              1                8
  T2              2               45
  T3              3              146
  T4              1               17
[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
  RWDD2B MUTATED     7   0   0
  RWDD2B WILD-TYPE 126  44  46
D36V6, multiclass
    clus
vv   RWDD2B MUTATED RWDD2B WILD-TYPE
  N0              7              126
  N1              0               44
  N2              0               46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  RWDD2B MUTATED     6   0   0
  RWDD2B WILD-TYPE 183  31   1
D36V7, multiclass
     clus
vv    RWDD2B MUTATED RWDD2B WILD-TYPE
  M0               6              183
  M1               0               31
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                  cls
clus                 0   1
  RWDD2B MUTATED     4   3
  RWDD2B WILD-TYPE 103 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD2B MUTATED      4    3
  RWDD2B WILD-TYPE  103  113
        clus
vv       RWDD2B MUTATED RWDD2B WILD-TYPE
  FEMALE              4              103
  MALE                3              113
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RWDD2B MUTATED                      5                             0
  RWDD2B WILD-TYPE                  125                            22
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RWDD2B MUTATED                       2                              0
  RWDD2B WILD-TYPE                    55                              8
D36V9, multiclass
                                clus
vv                               RWDD2B MUTATED RWDD2B WILD-TYPE
  COLON ADENOCARCINOMA                        5              125
  COLON MUCINOUS ADENOCARCINOMA               0               22
  RECTAL ADENOCARCINOMA                       2               55
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RWDD2B MUTATED     6   0   0   0
  RWDD2B WILD-TYPE 181   2  27   1
D36V10, multiclass
    clus
vv   RWDD2B MUTATED RWDD2B WILD-TYPE
  R0              6              181
  R1              0                2
  R2              0               27
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous

Clustering(37) Variable = TBC1D10C MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     3   0
  TBC1D10C WILD-TYPE 166  35
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                201 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 0                 35 
$`TBC1D10C MUTATED`
TCGA-AA-3821 TCGA-AA-3949 TCGA-AA-3971 
        1.02        26.01        16.08 

$`TBC1D10C WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        33.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.02               0.92 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             26.01             117.11 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             16.08              20.98 
[1] "1.0 - 26.0 (16.1)"  "0.9 - 117.1 (21.0)"
[1] "hr="     "9100000"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     3   0
  TBC1D10C WILD-TYPE 150  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      3    0
  TBC1D10C WILD-TYPE  150   68
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON                 3                150
  RECTUM                0                 68
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TBC1D10C MUTATED         1        0         0         0         1          0
  TBC1D10C WILD-TYPE      48       20        57         4        17          2
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBC1D10C MUTATED            1          0        0         0
  TBC1D10C WILD-TYPE         19         20       31         1
D37V4, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                 48
  STAGE II                  0                 20
  STAGE IIA                 0                 57
  STAGE IIB                 0                  4
  STAGE III                 1                 17
  STAGE IIIA                0                  2
  STAGE IIIB                1                 19
  STAGE IIIC                0                 20
  STAGE IV                  0                 31
  STAGE IVA                 0                  1
[1] 10  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
  TBC1D10C MUTATED     0   1   2   0
  TBC1D10C WILD-TYPE   9  46 147  18
D37V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                0                  9
  T2                1                 46
  T3                2                147
  T4                0                 18
[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
  TBC1D10C MUTATED     1   2   0
  TBC1D10C WILD-TYPE 132  42  46
D37V6, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                1                132
  N1                2                 42
  N2                0                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A
  TBC1D10C MUTATED     3   0   0
  TBC1D10C WILD-TYPE 186  31   1
D37V7, multiclass
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  M0                 3                186
  M1                 0                 31
  M1A                0                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     2   1
  TBC1D10C WILD-TYPE 105 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      2    1
  TBC1D10C WILD-TYPE  105  115
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                2                105
  MALE                  1                115
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBC1D10C MUTATED                      1                             2
  TBC1D10C WILD-TYPE                  129                            20
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBC1D10C MUTATED                       0                              0
  TBC1D10C WILD-TYPE                    57                              8
D37V9, multiclass
                                clus
vv                               TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON ADENOCARCINOMA                          1                129
  COLON MUCINOUS ADENOCARCINOMA                 2                 20
  RECTAL ADENOCARCINOMA                         0                 57
  RECTAL MUCINOUS ADENOCARCINOMA                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TBC1D10C MUTATED     3   0   0   0
  TBC1D10C WILD-TYPE 184   2  27   1
D37V10, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                3                184
  R1                0                  2
  R2                0                 27
  RX                0                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous

Clustering(38) Variable = ERCC6L MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  ERCC6L MUTATED     3   1
  ERCC6L WILD-TYPE 166  34
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               4              200 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               1               34 
$`ERCC6L MUTATED`
TCGA-A6-2672 TCGA-AA-3860 TCGA-AA-A01D TCGA-AG-3892 
       46.65        31.07         0.99        13.02 

$`ERCC6L WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        23.38        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  ERCC6L MUTATED ERCC6L WILD-TYPE 
            0.99             0.92 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
           46.65           117.11 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          22.045           20.485 
[1] "1.0 - 46.6 (22.0)"  "0.9 - 117.1 (20.5)"
[1] "hr=" "1.4"
D38V2, continuous
D38V3, binary
                  cls
clus                 0   1
  ERCC6L MUTATED     4   1
  ERCC6L WILD-TYPE 149  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED      4    1
  ERCC6L WILD-TYPE  149   67
        clus
vv       ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON               4              149
  RECTUM              1               67
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ERCC6L MUTATED         1        0         1         0         0          0
  ERCC6L WILD-TYPE      48       20        56         4        18          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC6L MUTATED            2          1        0         0
  ERCC6L WILD-TYPE         18         19       31         1
D38V4, multiclass
            clus
vv           ERCC6L MUTATED ERCC6L WILD-TYPE
  STAGE I                 1               48
  STAGE II                0               20
  STAGE IIA               1               56
  STAGE IIB               0                4
  STAGE III               0               18
  STAGE IIIA              0                2
  STAGE IIIB              2               18
  STAGE IIIC              1               19
  STAGE IV                0               31
  STAGE IVA               0                1
[1] 10  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
  ERCC6L MUTATED     1   0   4   0
  ERCC6L WILD-TYPE   8  47 145  18
D38V5, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  T1              1                8
  T2              0               47
  T3              4              145
  T4              0               18
[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
  ERCC6L MUTATED     2   2   1
  ERCC6L WILD-TYPE 131  42  45
D38V6, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  N0              2              131
  N1              2               42
  N2              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A
  ERCC6L MUTATED     5   0   0
  ERCC6L WILD-TYPE 184  31   1
D38V7, multiclass
     clus
vv    ERCC6L MUTATED ERCC6L WILD-TYPE
  M0               5              184
  M1               0               31
  M1A              0                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                  cls
clus                 0   1
  ERCC6L MUTATED     5   0
  ERCC6L WILD-TYPE 102 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED      5    0
  ERCC6L WILD-TYPE  102  116
        clus
vv       ERCC6L MUTATED ERCC6L WILD-TYPE
  FEMALE              5              102
  MALE                0              116
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERCC6L MUTATED                      3                             1
  ERCC6L WILD-TYPE                  127                            21
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERCC6L MUTATED                       1                              0
  ERCC6L WILD-TYPE                    56                              8
D38V9, multiclass
                                clus
vv                               ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON ADENOCARCINOMA                        3              127
  COLON MUCINOUS ADENOCARCINOMA               1               21
  RECTAL ADENOCARCINOMA                       1               56
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ERCC6L MUTATED     5   0   0   0
  ERCC6L WILD-TYPE 182   2  27   1
D38V10, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  R0              5              182
  R1              0                2
  R2              0               27
  RX              0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous

Clustering(39) Variable = ERBB3 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    11   1
  ERBB3 WILD-TYPE 158  34
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             12             192 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              1              34 
$`ERBB3 MUTATED`
TCGA-AA-3519 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-3976 
        9.07         0.92         0.99        25.02        53.00        26.01 
TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-A02N 
       38.04         0.99        34.98         6.05         7.99        61.97 

$`ERBB3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       19.99        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
        5.03        26.99         0.99        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 
       12.03         0.99        15.95        19.99        19.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.92            0.92 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          61.97          117.11 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         17.045          20.485 
[1] "0.9 - 62.0 (17.0)"  "0.9 - 117.1 (20.5)"
[1] "hr=" "1.9"
D39V2, continuous
D39V3, binary
                 cls
clus                0   1
  ERBB3 MUTATED    11   3
  ERBB3 WILD-TYPE 142  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     11    3
  ERBB3 WILD-TYPE  142   65
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON             11             142
  RECTUM             3              65
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ERBB3 MUTATED         2        4         2         1         2          1
  ERBB3 WILD-TYPE      47       16        55         3        16          1
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB3 MUTATED            0          1        1         0
  ERBB3 WILD-TYPE         20         19       30         1
D39V4, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                2              47
  STAGE II               4              16
  STAGE IIA              2              55
  STAGE IIB              1               3
  STAGE III              2              16
  STAGE IIIA             1               1
  STAGE IIIB             0              20
  STAGE IIIC             1              19
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  ERBB3 MUTATED     0   3   9   2
  ERBB3 WILD-TYPE   9  44 140  16
D39V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             0               9
  T2             3              44
  T3             9             140
  T4             2              16
[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
  ERBB3 MUTATED     9   3   2
  ERBB3 WILD-TYPE 124  41  44
D39V6, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0             9             124
  N1             3              41
  N2             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  ERBB3 MUTATED    13   1   0
  ERBB3 WILD-TYPE 176  30   1
D39V7, multiclass
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  M0             13             176
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED     7   7
  ERBB3 WILD-TYPE 100 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      7    7
  ERBB3 WILD-TYPE  100  109
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE             7             100
  MALE               7             109
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB3 MUTATED                     11                             0
  ERBB3 WILD-TYPE                  119                            22
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB3 MUTATED                       3                              0
  ERBB3 WILD-TYPE                    54                              8
D39V9, multiclass
                                clus
vv                               ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON ADENOCARCINOMA                      11             119
  COLON MUCINOUS ADENOCARCINOMA              0              22
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    13   0   1   0
  ERBB3 WILD-TYPE 174   2  26   1
D39V10, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            13             174
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous

Clustering(40) Variable = KLK2 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  KLK2 MUTATED     3   0
  KLK2 WILD-TYPE 166  35
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            201 
  KLK2 MUTATED KLK2 WILD-TYPE 
             0             35 
$`KLK2 MUTATED`
TCGA-AA-3542 TCGA-AA-3555 TCGA-AA-A00A 
       12.99        29.95        38.04 

$`KLK2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  KLK2 MUTATED KLK2 WILD-TYPE 
         12.99           0.92 
  KLK2 MUTATED KLK2 WILD-TYPE 
         38.04         117.11 
  KLK2 MUTATED KLK2 WILD-TYPE 
         29.95          19.99 
[1] "13.0 - 38.0 (29.9)" "0.9 - 117.1 (20.0)"
[1] "hr="     "9100000"
D40V2, continuous
D40V3, binary
                cls
clus               0   1
  KLK2 MUTATED     3   0
  KLK2 WILD-TYPE 150  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK2 MUTATED      3    0
  KLK2 WILD-TYPE  150   68
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  COLON             3            150
  RECTUM            0             68
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KLK2 MUTATED         0        0         2         0         0          0
  KLK2 WILD-TYPE      49       20        55         4        18          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLK2 MUTATED            0          1        0         0
  KLK2 WILD-TYPE         20         19       31         1
D40V4, multiclass
            clus
vv           KLK2 MUTATED KLK2 WILD-TYPE
  STAGE I               0             49
  STAGE II              0             20
  STAGE IIA             2             55
  STAGE IIB             0              4
  STAGE III             0             18
  STAGE IIIA            0              2
  STAGE IIIB            0             20
  STAGE IIIC            1             19
  STAGE IV              0             31
  STAGE IVA             0              1
[1] 10  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
  KLK2 MUTATED     0   0   3   0
  KLK2 WILD-TYPE   9  47 146  18
D40V5, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  T1            0              9
  T2            0             47
  T3            3            146
  T4            0             18
[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
  KLK2 MUTATED     2   0   1
  KLK2 WILD-TYPE 131  44  45
D40V6, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  N0            2            131
  N1            0             44
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  KLK2 MUTATED     3   0   0
  KLK2 WILD-TYPE 186  31   1
D40V7, multiclass
     clus
vv    KLK2 MUTATED KLK2 WILD-TYPE
  M0             3            186
  M1             0             31
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                cls
clus               0   1
  KLK2 MUTATED     1   2
  KLK2 WILD-TYPE 106 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK2 MUTATED      1    2
  KLK2 WILD-TYPE  106  114
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  FEMALE            1            106
  MALE              2            114
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLK2 MUTATED                      2                             1
  KLK2 WILD-TYPE                  128                            21
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLK2 MUTATED                       0                              0
  KLK2 WILD-TYPE                    57                              8
D40V9, multiclass
                                clus
vv                               KLK2 MUTATED KLK2 WILD-TYPE
  COLON ADENOCARCINOMA                      2            128
  COLON MUCINOUS ADENOCARCINOMA             1             21
  RECTAL ADENOCARCINOMA                     0             57
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLK2 MUTATED     3   0   0   0
  KLK2 WILD-TYPE 184   2  27   1
D40V10, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  R0            3            184
  R1            0              2
  R2            0             27
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous

Clustering(41) Variable = TAPBP MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  TAPBP MUTATED     5   0
  TAPBP WILD-TYPE 164  35
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             199 
  TAPBP MUTATED TAPBP WILD-TYPE 
              0              35 
$`TAPBP MUTATED`
TCGA-AA-3833 TCGA-AA-A00J TCGA-AA-A010 TCGA-AG-3593 TCGA-AG-3892 
       15.95        18.05        34.98        34.03        13.02 

$`TAPBP WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 
      117.11 

  TAPBP MUTATED TAPBP WILD-TYPE 
          13.02            0.92 
  TAPBP MUTATED TAPBP WILD-TYPE 
          34.98          117.11 
  TAPBP MUTATED TAPBP WILD-TYPE 
          18.05           20.98 
[1] "13.0 - 35.0 (18.1)" "0.9 - 117.1 (21.0)"
[1] "hr="     "9300000"
D41V2, continuous
D41V3, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   2
  TAPBP WILD-TYPE 150  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    2
  TAPBP WILD-TYPE  150   66
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  COLON              3             150
  RECTUM             2              66
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TAPBP MUTATED         1        0         2         1         0          0
  TAPBP WILD-TYPE      48       20        55         3        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAPBP MUTATED            1          0        0         0
  TAPBP WILD-TYPE         19         20       31         1
D41V4, multiclass
            clus
vv           TAPBP MUTATED TAPBP WILD-TYPE
  STAGE I                1              48
  STAGE II               0              20
  STAGE IIA              2              55
  STAGE IIB              1               3
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             1              19
  STAGE IIIC             0              20
  STAGE IV               0              31
  STAGE IVA              0               1
[1] 10  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
  TAPBP MUTATED     1   0   2   2
  TAPBP WILD-TYPE   8  47 147  16
D41V5, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  T1             1               8
  T2             0              47
  T3             2             147
  T4             2              16
[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
  TAPBP MUTATED     4   1   0
  TAPBP WILD-TYPE 129  43  46
D41V6, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  N0             4             129
  N1             1              43
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  TAPBP MUTATED     5   0   0
  TAPBP WILD-TYPE 184  31   1
D41V7, multiclass
     clus
vv    TAPBP MUTATED TAPBP WILD-TYPE
  M0              5             184
  M1              0              31
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                 cls
clus                0   1
  TAPBP MUTATED     4   1
  TAPBP WILD-TYPE 103 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      4    1
  TAPBP WILD-TYPE  103  115
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  FEMALE             4             103
  MALE               1             115
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAPBP MUTATED                      2                             1
  TAPBP WILD-TYPE                  128                            21
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAPBP MUTATED                       2                              0
  TAPBP WILD-TYPE                    55                              8
D41V9, multiclass
                                clus
vv                               TAPBP MUTATED TAPBP WILD-TYPE
  COLON ADENOCARCINOMA                       2             128
  COLON MUCINOUS ADENOCARCINOMA              1              21
  RECTAL ADENOCARCINOMA                      2              55
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAPBP MUTATED     5   0   0   0
  TAPBP WILD-TYPE 182   2  27   1
D41V10, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  R0             5             182
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous

Clustering(42) Variable = ERBB2 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     8   1
  ERBB2 WILD-TYPE 161  34
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             195 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              1              34 
$`ERBB2 MUTATED`
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AG-3599 
       53.00        27.02        33.01        25.02        27.02        12.03 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-A00Y 
       48.03        32.02        23.01 

$`ERBB2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 
       18.05        40.96        16.31         0.95        17.95        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       13.55        12.72        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01         1.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
          12.03            0.92 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          53.00          117.11 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          27.02           19.99 
[1] "12.0 - 53.0 (27.0)" "0.9 - 117.1 (20.0)"
[1] "hr=" "2"  
D42V2, continuous
D42V3, binary
                 cls
clus                0   1
  ERBB2 MUTATED     5   4
  ERBB2 WILD-TYPE 148  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      5    4
  ERBB2 WILD-TYPE  148   64
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON              5             148
  RECTUM             4              64
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ERBB2 MUTATED         1        1         3         1         0          0
  ERBB2 WILD-TYPE      48       19        54         3        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED            1          0        1         0
  ERBB2 WILD-TYPE         19         20       30         1
D42V4, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                1              48
  STAGE II               1              19
  STAGE IIA              3              54
  STAGE IIB              1               3
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             1              19
  STAGE IIIC             0              20
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  ERBB2 MUTATED     0   2   5   2
  ERBB2 WILD-TYPE   9  45 144  16
D42V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0               9
  T2             2              45
  T3             5             144
  T4             2              16
[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
  ERBB2 MUTATED     7   1   1
  ERBB2 WILD-TYPE 126  43  45
D42V6, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             7             126
  N1             1              43
  N2             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  ERBB2 MUTATED     7   1   0
  ERBB2 WILD-TYPE 182  30   1
D42V7, multiclass
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  M0              7             182
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1   8
  ERBB2 WILD-TYPE 106 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1    8
  ERBB2 WILD-TYPE  106  108
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             1             106
  MALE               8             108
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB2 MUTATED                      3                             2
  ERBB2 WILD-TYPE                  127                            20
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB2 MUTATED                       3                              0
  ERBB2 WILD-TYPE                    54                              8
D42V9, multiclass
                                clus
vv                               ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             127
  COLON MUCINOUS ADENOCARCINOMA              2              20
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     7   0   1   0
  ERBB2 WILD-TYPE 180   2  26   1
D42V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             7             180
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous

Clustering(43) Variable = MORC2 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  MORC2 MUTATED     4   1
  MORC2 WILD-TYPE 165  34
  MORC2 MUTATED MORC2 WILD-TYPE 
              5             199 
  MORC2 MUTATED MORC2 WILD-TYPE 
              1              34 
$`MORC2 MUTATED`
TCGA-AA-3542 TCGA-AA-3811 TCGA-AA-A00R TCGA-AG-3892 TCGA-AG-A002 
       12.99         0.99         0.99        13.02        20.98 

$`MORC2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 
      117.11 

  MORC2 MUTATED MORC2 WILD-TYPE 
           0.99            0.92 
  MORC2 MUTATED MORC2 WILD-TYPE 
          20.98          117.11 
  MORC2 MUTATED MORC2 WILD-TYPE 
          12.99           20.98 
[1] "1.0 - 21.0 (13.0)"  "0.9 - 117.1 (21.0)"
[1] "hr=" "2.3"
D43V2, continuous
D43V3, binary
                 cls
clus                0   1
  MORC2 MUTATED     3   2
  MORC2 WILD-TYPE 150  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      3    2
  MORC2 WILD-TYPE  150   66
        clus
vv       MORC2 MUTATED MORC2 WILD-TYPE
  COLON              3             150
  RECTUM             2              66
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MORC2 MUTATED         3        0         0         0         1          0
  MORC2 WILD-TYPE      46       20        57         4        17          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MORC2 MUTATED            0          1        0         0
  MORC2 WILD-TYPE         20         19       31         1
D43V4, multiclass
            clus
vv           MORC2 MUTATED MORC2 WILD-TYPE
  STAGE I                3              46
  STAGE II               0              20
  STAGE IIA              0              57
  STAGE IIB              0               4
  STAGE III              1              17
  STAGE IIIA             0               2
  STAGE IIIB             0              20
  STAGE IIIC             1              19
  STAGE IV               0              31
  STAGE IVA              0               1
[1] 10  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
  MORC2 MUTATED     1   2   2   0
  MORC2 WILD-TYPE   8  45 147  18
D43V5, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  T1             1               8
  T2             2              45
  T3             2             147
  T4             0              18
[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
  MORC2 MUTATED     3   0   2
  MORC2 WILD-TYPE 130  44  44
D43V6, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  N0             3             130
  N1             0              44
  N2             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  MORC2 MUTATED     5   0   0
  MORC2 WILD-TYPE 184  31   1
D43V7, multiclass
     clus
vv    MORC2 MUTATED MORC2 WILD-TYPE
  M0              5             184
  M1              0              31
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                 cls
clus                0   1
  MORC2 MUTATED     3   2
  MORC2 WILD-TYPE 104 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      3    2
  MORC2 WILD-TYPE  104  114
        clus
vv       MORC2 MUTATED MORC2 WILD-TYPE
  FEMALE             3             104
  MALE               2             114
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MORC2 MUTATED                      3                             0
  MORC2 WILD-TYPE                  127                            22
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MORC2 MUTATED                       2                              0
  MORC2 WILD-TYPE                    55                              8
D43V9, multiclass
                                clus
vv                               MORC2 MUTATED MORC2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             127
  COLON MUCINOUS ADENOCARCINOMA              0              22
  RECTAL ADENOCARCINOMA                      2              55
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC2 MUTATED     5   0   0   0
  MORC2 WILD-TYPE 182   2  27   1
D43V10, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  R0             5             182
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous

Clustering(44) Variable = ABCA8 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  ABCA8 MUTATED     8   2
  ABCA8 WILD-TYPE 161  33
  ABCA8 MUTATED ABCA8 WILD-TYPE 
             10             194 
  ABCA8 MUTATED ABCA8 WILD-TYPE 
              2              33 
$`ABCA8 MUTATED`
TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       26.99        31.00        26.01         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AF-3913 TCGA-AG-3893 TCGA-AG-A002 
       34.98        10.39        35.01        20.98 

$`ABCA8 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       16.31         0.95        17.95        43.04        13.55        12.72 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       19.99         7.99         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  ABCA8 MUTATED ABCA8 WILD-TYPE 
           2.01            0.92 
  ABCA8 MUTATED ABCA8 WILD-TYPE 
          35.01          117.11 
  ABCA8 MUTATED ABCA8 WILD-TYPE 
         25.515          19.990 
[1] "2.0 - 35.0 (25.5)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
                 cls
clus                0   1
  ABCA8 MUTATED     8   4
  ABCA8 WILD-TYPE 145  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA8 MUTATED      8    4
  ABCA8 WILD-TYPE  145   64
        clus
vv       ABCA8 MUTATED ABCA8 WILD-TYPE
  COLON              8             145
  RECTUM             4              64
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ABCA8 MUTATED         2        0         3         2         0          0
  ABCA8 WILD-TYPE      47       20        54         2        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCA8 MUTATED            3          0        1         0
  ABCA8 WILD-TYPE         17         20       30         1
D44V4, multiclass
            clus
vv           ABCA8 MUTATED ABCA8 WILD-TYPE
  STAGE I                2              47
  STAGE II               0              20
  STAGE IIA              3              54
  STAGE IIB              2               2
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             3              17
  STAGE IIIC             0              20
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  ABCA8 MUTATED     1   2   7   2
  ABCA8 WILD-TYPE   8  45 142  16
D44V5, multiclass
    clus
vv   ABCA8 MUTATED ABCA8 WILD-TYPE
  T1             1               8
  T2             2              45
  T3             7             142
  T4             2              16
[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
  ABCA8 MUTATED     8   4   0
  ABCA8 WILD-TYPE 125  40  46
D44V6, multiclass
    clus
vv   ABCA8 MUTATED ABCA8 WILD-TYPE
  N0             8             125
  N1             4              40
  N2             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  ABCA8 MUTATED    10   1   0
  ABCA8 WILD-TYPE 179  30   1
D44V7, multiclass
     clus
vv    ABCA8 MUTATED ABCA8 WILD-TYPE
  M0             10             179
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                 cls
clus                0   1
  ABCA8 MUTATED     7   5
  ABCA8 WILD-TYPE 100 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA8 MUTATED      7    5
  ABCA8 WILD-TYPE  100  111
        clus
vv       ABCA8 MUTATED ABCA8 WILD-TYPE
  FEMALE             7             100
  MALE               5             111
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCA8 MUTATED                      4                             4
  ABCA8 WILD-TYPE                  126                            18
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCA8 MUTATED                       3                              1
  ABCA8 WILD-TYPE                    54                              7
D44V9, multiclass
                                clus
vv                               ABCA8 MUTATED ABCA8 WILD-TYPE
  COLON ADENOCARCINOMA                       4             126
  COLON MUCINOUS ADENOCARCINOMA              4              18
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCA8 MUTATED    10   0   0   0
  ABCA8 WILD-TYPE 177   2  27   1
D44V10, multiclass
    clus
vv   ABCA8 MUTATED ABCA8 WILD-TYPE
  R0            10             177
  R1             0               2
  R2             0              27
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous

Clustering(45) Variable = SETD2 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    10   2
  SETD2 WILD-TYPE 159  33
  SETD2 MUTATED SETD2 WILD-TYPE 
             12             192 
  SETD2 MUTATED SETD2 WILD-TYPE 
              2              33 
$`SETD2 MUTATED`
TCGA-A6-2672 TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3680 TCGA-AA-3710 
       46.65         8.05        12.99         0.99        11.01        26.99 
TCGA-AA-3851 TCGA-AA-A00E TCGA-AA-A00N TCGA-AF-2691 TCGA-AG-3892 TCGA-AG-A002 
       33.07        30.02         4.01        43.04        13.02        20.98 

$`SETD2 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        23.38        17.79        42.28        15.52        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       33.34        36.53         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        37.05        36.03        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 
       20.98        19.99        13.94        19.99        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 
       37.05        19.00        36.00         5.03         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        37.02        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        17.03        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       41.00        39.98        18.05        40.96        16.31         0.95 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       17.95        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.99            0.92 
  SETD2 MUTATED SETD2 WILD-TYPE 
          46.65          117.11 
  SETD2 MUTATED SETD2 WILD-TYPE 
         17.000          20.485 
[1] "1.0 - 46.6 (17.0)"  "0.9 - 117.1 (20.5)"
[1] "hr=" "1"  
D45V2, continuous
D45V3, binary
                 cls
clus                0   1
  SETD2 MUTATED    10   3
  SETD2 WILD-TYPE 143  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     10    3
  SETD2 WILD-TYPE  143   65
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  COLON             10             143
  RECTUM             3              65
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SETD2 MUTATED         4        0         4         1         0          0
  SETD2 WILD-TYPE      45       20        53         3        18          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD2 MUTATED            2          1        1         0
  SETD2 WILD-TYPE         18         19       30         1
D45V4, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                4              45
  STAGE II               0              20
  STAGE IIA              4              53
  STAGE IIB              1               3
  STAGE III              0              18
  STAGE IIIA             0               2
  STAGE IIIB             2              18
  STAGE IIIC             1              19
  STAGE IV               1              30
  STAGE IVA              0               1
[1] 10  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
  SETD2 MUTATED     2   2   7   2
  SETD2 WILD-TYPE   7  45 142  16
D45V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             2               7
  T2             2              45
  T3             7             142
  T4             2              16
[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
  SETD2 MUTATED     9   2   2
  SETD2 WILD-TYPE 124  42  44
D45V6, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0             9             124
  N1             2              42
  N2             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A
  SETD2 MUTATED    12   1   0
  SETD2 WILD-TYPE 177  30   1
D45V7, multiclass
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  M0             12             177
  M1              1              30
  M1A             0               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                 cls
clus                0   1
  SETD2 MUTATED     6   7
  SETD2 WILD-TYPE 101 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      6    7
  SETD2 WILD-TYPE  101  109
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             6             101
  MALE               7             109
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SETD2 MUTATED                      8                             2
  SETD2 WILD-TYPE                  122                            20
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SETD2 MUTATED                       3                              0
  SETD2 WILD-TYPE                    54                              8
D45V9, multiclass
                                clus
vv                               SETD2 MUTATED SETD2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             122
  COLON MUCINOUS ADENOCARCINOMA              2              20
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    12   0   1   0
  SETD2 WILD-TYPE 175   2  26   1
D45V10, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            12             175
  R1             0               2
  R2             1              26
  RX             0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous

Clustering(46) Variable = ESR1 MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  ESR1 MUTATED     9   1
  ESR1 WILD-TYPE 160  34
  ESR1 MUTATED ESR1 WILD-TYPE 
            10            194 
  ESR1 MUTATED ESR1 WILD-TYPE 
             1             34 
$`ESR1 MUTATED`
TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3858 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 
        8.05        12.99        31.07        33.01        26.01        25.02 
TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       27.02         4.01        34.98         1.02 

$`ESR1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       34.65        33.34        36.53         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 
       13.05        34.06        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        17.03        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AF-2689 
       39.98        18.05        40.96        16.31         0.95        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  ESR1 MUTATED ESR1 WILD-TYPE 
          1.02           0.92 
  ESR1 MUTATED ESR1 WILD-TYPE 
         34.98         117.11 
  ESR1 MUTATED ESR1 WILD-TYPE 
        25.515         19.990 
[1] "1.0 - 35.0 (25.5)"  "0.9 - 117.1 (20.0)"
[1] "hr=" "1.5"
D46V2, continuous
D46V3, binary
                cls
clus               0   1
  ESR1 MUTATED    11   0
  ESR1 WILD-TYPE 142  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     11    0
  ESR1 WILD-TYPE  142   68
        clus
vv       ESR1 MUTATED ESR1 WILD-TYPE
  COLON            11            142
  RECTUM            0             68
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ESR1 MUTATED         1        2         0         3         0          0
  ESR1 WILD-TYPE      48       18        57         1        18          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESR1 MUTATED            3          1        0         0
  ESR1 WILD-TYPE         17         19       31         1
D46V4, multiclass
            clus
vv           ESR1 MUTATED ESR1 WILD-TYPE
  STAGE I               1             48
  STAGE II              2             18
  STAGE IIA             0             57
  STAGE IIB             3              1
  STAGE III             0             18
  STAGE IIIA            0              2
  STAGE IIIB            3             17
  STAGE IIIC            1             19
  STAGE IV              0             31
  STAGE IVA             0              1
[1] 10  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
  ESR1 MUTATED     0   2   5   4
  ESR1 WILD-TYPE   9  45 144  14
D46V5, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  T1            0              9
  T2            2             45
  T3            5            144
  T4            4             14
[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
  ESR1 MUTATED     7   3   1
  ESR1 WILD-TYPE 126  41  45
D46V6, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  N0            7            126
  N1            3             41
  N2            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A
  ESR1 MUTATED    10   0   0
  ESR1 WILD-TYPE 179  31   1
D46V7, multiclass
     clus
vv    ESR1 MUTATED ESR1 WILD-TYPE
  M0            10            179
  M1             0             31
  M1A            0              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                cls
clus               0   1
  ESR1 MUTATED     5   6
  ESR1 WILD-TYPE 102 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED      5    6
  ESR1 WILD-TYPE  102  110
        clus
vv       ESR1 MUTATED ESR1 WILD-TYPE
  FEMALE            5            102
  MALE              6            110
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESR1 MUTATED                      8                             3
  ESR1 WILD-TYPE                  122                            19
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESR1 MUTATED                       0                              0
  ESR1 WILD-TYPE                    57                              8
D46V9, multiclass
                                clus
vv                               ESR1 MUTATED ESR1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            122
  COLON MUCINOUS ADENOCARCINOMA             3             19
  RECTAL ADENOCARCINOMA                     0             57
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ESR1 MUTATED     9   0   0   0
  ESR1 WILD-TYPE 178   2  27   1
D46V10, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  R0            9            178
  R1            0              2
  R2            0             27
  RX            0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
