[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"        "-oTCOAD-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/COAD-TP/10005863/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/10687005/transformed.cor.cli.txt"

nPatients in clinical file=441, in cluster file=154, common to both=154
[1]  27 154
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          107            47 
  APC MUTATED APC WILD-TYPE 
          107            47 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            73             81 
  TP53 MUTATED TP53 WILD-TYPE 
            73             81 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            59             95 
  KRAS MUTATED KRAS WILD-TYPE 
            59             95 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
[1] "MGC42105 MUTATION ANALYSIS"
[1] 3
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                10                144 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                10                144 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              141 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              141 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             12             142 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             12             142 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             10             144 
  CDC27 MUTATED CDC27 WILD-TYPE 
             10             144 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
             6            148 
  BCOR MUTATED BCOR WILD-TYPE 
             6            148 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             8            146 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             8            146 
[1] "KLHL5 MUTATION ANALYSIS"
[1] 3
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              5             149 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              5             149 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             144 
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             144 
[1] "PCDHGB1 MUTATION ANALYSIS"
[1] 3
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                7               147 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                7               147 
[1] "UBXN11 MUTATION ANALYSIS"
[1] 3
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               3              151 
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               3              151 
[1] "MIER3 MUTATION ANALYSIS"
[1] 3
  MIER3 MUTATED MIER3 WILD-TYPE 
             10             144 
  MIER3 MUTATED MIER3 WILD-TYPE 
             10             144 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                151 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                151 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              11              143 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              11              143 
[1] "PCDHGA9 MUTATION ANALYSIS"
[1] 3
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                5               149 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                5               149 
[1] "PCDHGA7 MUTATION ANALYSIS"
[1] 3
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               149 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               149 
[1] "KLK2 MUTATION ANALYSIS"
[1] 3
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            151 
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            151 
[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 154 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 
          NA         1246           NA           NA 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=76,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	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=15,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
[3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
[5] "PATHOLOGY.M.STAGE"         "GENDER"                   
[7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
[9] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 154 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
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 
  4  33 102  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  4  33 102  15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  4  33 102  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  4  33 102  15 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
90 30 34 
[1] "table(vv)"
vv
N0 N1 N2 
90 30 34 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
90 30 34 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
90 30 34 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=15, binary=FALSE, numeric=TRUE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  APC MUTATED   80 17
  APC WILD-TYPE 35  9
  APC MUTATED APC WILD-TYPE 
           97            44 
  APC MUTATED APC WILD-TYPE 
           17             9 
$`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 
        0.95 

$`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 
       40.96        16.31 

  APC MUTATED APC WILD-TYPE 
         0.92          0.92 
  APC MUTATED APC WILD-TYPE 
        53.00         54.02 
  APC MUTATED APC WILD-TYPE 
        24.00         19.53 
[1] "0.9 - 53.0 (24.0)" "0.9 - 54.0 (19.5)"
[1] "hr=" "1.2"
D1V2, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  APC MUTATED        21       10        27         3        10          1
  APC WILD-TYPE      10        4        11         1         4          1
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED            6         10       17         1
  APC WILD-TYPE          6          6        4         0
D1V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             21            10
  STAGE II            10             4
  STAGE IIA           27            11
  STAGE IIB            3             1
  STAGE III           10             4
  STAGE IIIA           1             1
  STAGE IIIB           6             6
  STAGE IIIC          10             6
  STAGE IV            17             4
  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    2 23 72 10
  APC WILD-TYPE  2 10 30  5
D1V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           2             2
  T2          23            10
  T3          72            30
  T4          10             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   63 21 23
  APC WILD-TYPE 27  9 11
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          63            27
  N1          21             9
  N2          23            11
[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   87 17   1
  APC WILD-TYPE 43  4   0
D1V6, multiclass
     clus
vv    APC MUTATED APC WILD-TYPE
  M0           87            43
  M1           17             4
  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"
D1V7, binary
               cls
clus             0  1
  APC MUTATED   46 61
  APC WILD-TYPE 31 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     46   61
  APC WILD-TYPE   31   16
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          46            31
  MALE            61            16
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus             0  1
  APC MUTATED   91 14
  APC WILD-TYPE 39  8
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     91   14
  APC WILD-TYPE   39    8
                               clus
vv                              APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                   91            39
  COLON MUCINOUS ADENOCARCINOMA          14             8
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2 RX
  APC MUTATED   87  0 16  1
  APC WILD-TYPE 41  1  3  0
D1V9, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          87            41
  R1           0             1
  R2          16             3
  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"
D1V10, continuous

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   58 13
  TP53 WILD-TYPE 57 13
  TP53 MUTATED TP53 WILD-TYPE 
            71             70 
  TP53 MUTATED TP53 WILD-TYPE 
            13             13 
$`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 
        5.03        41.00        40.96        16.31         0.95 

$`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 
       51.98         0.92        39.98        18.05 

  TP53 MUTATED TP53 WILD-TYPE 
          0.95           0.92 
  TP53 MUTATED TP53 WILD-TYPE 
         50.99          54.02 
  TP53 MUTATED TP53 WILD-TYPE 
         24.00          19.53 
[1] "0.9 - 51.0 (24.0)" "0.9 - 54.0 (19.5)"
[1] "hr=" "1"  
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TP53 MUTATED        16        4        13         2         6          2
  TP53 WILD-TYPE      15       10        25         2         8          0
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED            6         11       11         1
  TP53 WILD-TYPE          6          5       10         0
D2V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              16             15
  STAGE II              4             10
  STAGE IIA            13             25
  STAGE IIB             2              2
  STAGE III             6              8
  STAGE IIIA            2              0
  STAGE IIIB            6              6
  STAGE IIIC           11              5
  STAGE IV             11             10
  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    3 17 47  6
  TP53 WILD-TYPE  1 16 55  9
D2V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            3              1
  T2           17             16
  T3           47             55
  T4            6              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   38 16 19
  TP53 WILD-TYPE 52 14 15
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           38             52
  N1           16             14
  N2           19             15
[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   59 11   1
  TP53 WILD-TYPE 71 10   0
D2V6, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  M0            59             71
  M1            11             10
  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"
D2V7, binary
                cls
clus              0  1
  TP53 MUTATED   34 39
  TP53 WILD-TYPE 43 38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     34   39
  TP53 WILD-TYPE   43   38
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           34             43
  MALE             39             38
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED   67  4
  TP53 WILD-TYPE 63 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     67    4
  TP53 WILD-TYPE   63   18
                               clus
vv                              TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                    67             63
  COLON MUCINOUS ADENOCARCINOMA            4             18
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   59  1 10  0
  TP53 WILD-TYPE 69  0  9  1
D2V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           59             69
  R1            1              0
  R2           10              9
  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"
D2V10, continuous

Clustering(3) Variable = KRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   44  9
  KRAS WILD-TYPE 71 17
  KRAS MUTATED KRAS WILD-TYPE 
            53             88 
  KRAS MUTATED KRAS WILD-TYPE 
             9             17 
$`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 
        0.92        41.00        39.98        18.05        40.96 

$`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 
        2.01         5.03        16.31         0.95 

  KRAS MUTATED KRAS WILD-TYPE 
          0.92           0.95 
  KRAS MUTATED KRAS WILD-TYPE 
         53.00          54.02 
  KRAS MUTATED KRAS WILD-TYPE 
        25.020         20.485 
[1] "0.9 - 53.0 (25.0)" "0.9 - 54.0 (20.5)"
[1] "hr=" "1.2"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KRAS MUTATED        11        8        17         1         5          1
  KRAS WILD-TYPE      20        6        21         3         9          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED            3          5        6         1
  KRAS WILD-TYPE          9         11       15         0
D3V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              11             20
  STAGE II              8              6
  STAGE IIA            17             21
  STAGE IIB             1              3
  STAGE III             5              9
  STAGE IIIA            1              1
  STAGE IIIB            3              9
  STAGE IIIC            5             11
  STAGE IV              6             15
  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    1 13 40  5
  KRAS WILD-TYPE  3 20 62 10
D3V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            1              3
  T2           13             20
  T3           40             62
  T4            5             10
[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   39  9 11
  KRAS WILD-TYPE 51 21 23
D3V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           39             51
  N1            9             21
  N2           11             23
[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   51  6   1
  KRAS WILD-TYPE 79 15   0
D3V6, multiclass
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  M0            51             79
  M1             6             15
  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"
D3V7, binary
                cls
clus              0  1
  KRAS MUTATED   26 33
  KRAS WILD-TYPE 51 44
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     26   33
  KRAS WILD-TYPE   51   44
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           26             51
  MALE             33             44
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus              0  1
  KRAS MUTATED   49  9
  KRAS WILD-TYPE 81 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     49    9
  KRAS WILD-TYPE   81   13
                               clus
vv                              KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                    49             81
  COLON MUCINOUS ADENOCARCINOMA            9             13
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   52  0  5  1
  KRAS WILD-TYPE 76  1 14  0
D3V9, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           52             76
  R1            0              1
  R2            5             14
  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"
D3V10, continuous

Clustering(4) Variable = NRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    11   3
  NRAS WILD-TYPE 104  23
  NRAS MUTATED NRAS WILD-TYPE 
            14            127 
  NRAS MUTATED NRAS WILD-TYPE 
             3             23 
$`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 
       39.06        39.98 

$`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 
        0.95 

  NRAS MUTATED NRAS WILD-TYPE 
          2.01           0.92 
  NRAS MUTATED NRAS WILD-TYPE 
         53.00          54.02 
  NRAS MUTATED NRAS WILD-TYPE 
         30.02          21.99 
[1] "2.0 - 53.0 (30.0)" "0.9 - 54.0 (22.0)"
[1] "hr=" "1.1"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  NRAS MUTATED         4        2         1         1         1          1
  NRAS WILD-TYPE      27       12        37         3        13          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED            1          1        3         0
  NRAS WILD-TYPE         11         15       18         1
D4V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               4             27
  STAGE II              2             12
  STAGE IIA             1             37
  STAGE IIB             1              3
  STAGE III             1             13
  STAGE IIIA            1              1
  STAGE IIIB            1             11
  STAGE IIIC            1             15
  STAGE IV              3             18
  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    0  5  8  2
  NRAS WILD-TYPE  4 28 94 13
D4V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            0              4
  T2            5             28
  T3            8             94
  T4            2             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
  NRAS MUTATED    8  6  1
  NRAS WILD-TYPE 82 24 33
D4V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            8             82
  N1            6             24
  N2            1             33
[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    12   3   0
  NRAS WILD-TYPE 118  18   1
D4V6, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  M0            12            118
  M1             3             18
  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"
D4V7, binary
                cls
clus              0  1
  NRAS MUTATED    3 12
  NRAS WILD-TYPE 74 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      3   12
  NRAS WILD-TYPE   74   65
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            3             74
  MALE             12             65
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus               0   1
  NRAS MUTATED    13   2
  NRAS WILD-TYPE 117  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13    2
  NRAS WILD-TYPE  117   20
                               clus
vv                              NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                    13            117
  COLON MUCINOUS ADENOCARCINOMA            2             20
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    11   0   4   0
  NRAS WILD-TYPE 117   1  15   1
D4V9, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           11            117
  R1            0              1
  R2            4             15
  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"
D4V10, continuous

Clustering(5) Variable = SMAD4 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    11   5
  SMAD4 WILD-TYPE 104  21
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             16             125 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              5              21 
$`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 
       13.05        18.05         0.99         0.92 

$`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 
       39.98        18.05        40.96        16.31         0.95 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.92            0.92 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          53.00           54.02 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         20.025          24.000 
[1] "0.9 - 53.0 (20.0)" "0.9 - 54.0 (24.0)"
[1] "hr=" "2.1"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD4 MUTATED         3        3         5         1         2          0
  SMAD4 WILD-TYPE      28       11        33         3        12          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED            1          1        2         0
  SMAD4 WILD-TYPE         11         15       19         1
D5V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                3              28
  STAGE II               3              11
  STAGE IIA              5              33
  STAGE IIB              1               3
  STAGE III              2              12
  STAGE IIIA             0               2
  STAGE IIIB             1              11
  STAGE IIIC             1              15
  STAGE IV               2              19
  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  3 13  2
  SMAD4 WILD-TYPE  4 30 89 13
D5V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             0               4
  T2             3              30
  T3            13              89
  T4             2              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
  SMAD4 MUTATED   12  3  3
  SMAD4 WILD-TYPE 78 27 31
D5V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            12              78
  N1             3              27
  N2             3              31
[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    16   2   0
  SMAD4 WILD-TYPE 114  19   1
D5V6, multiclass
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  M0             16             114
  M1              2              19
  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"
D5V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED   10  8
  SMAD4 WILD-TYPE 67 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     10    8
  SMAD4 WILD-TYPE   67   69
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            10              67
  MALE               8              69
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    14   4
  SMAD4 WILD-TYPE 116  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     14    4
  SMAD4 WILD-TYPE  116   18
                               clus
vv                              SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                     14             116
  COLON MUCINOUS ADENOCARCINOMA             4              18
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    15   0   3   0
  SMAD4 WILD-TYPE 113   1  16   1
D5V9, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            15             113
  R1             0               1
  R2             3              16
  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"
D5V10, continuous

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED   18  6
  FBXW7 WILD-TYPE 97 20
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             24             117 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              6              20 
$`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 

$`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 
       40.96        16.31         0.95 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.92            0.92 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          46.65           54.02 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          19.02           24.00 
[1] "0.9 - 46.6 (19.0)" "0.9 - 54.0 (24.0)"
[1] "hr=" "1.6"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FBXW7 MUTATED         2        5         7         1         5          0
  FBXW7 WILD-TYPE      29        9        31         3         9          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED            4          5        0         0
  FBXW7 WILD-TYPE          8         11       21         1
D6V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                2              29
  STAGE II               5               9
  STAGE IIA              7              31
  STAGE IIB              1               3
  STAGE III              5               9
  STAGE IIIA             0               2
  STAGE IIIB             4               8
  STAGE IIIC             5              11
  STAGE IV               0              21
  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    0  2 24  3
  FBXW7 WILD-TYPE  4 31 78 12
D6V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             0               4
  T2             2              31
  T3            24              78
  T4             3              12
[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   15  6  8
  FBXW7 WILD-TYPE 75 24 26
D6V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            15              75
  N1             6              24
  N2             8              26
[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    29   0   0
  FBXW7 WILD-TYPE 101  21   1
D6V6, multiclass
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  M0             29             101
  M1              0              21
  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"
D6V7, binary
                 cls
clus               0  1
  FBXW7 MUTATED   18 11
  FBXW7 WILD-TYPE 59 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     18   11
  FBXW7 WILD-TYPE   59   66
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            18              59
  MALE              11              66
[1] 2 2
[1] FALSE
D6V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    20   9
  FBXW7 WILD-TYPE 110  13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     20    9
  FBXW7 WILD-TYPE  110   13
                               clus
vv                              FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                     20             110
  COLON MUCINOUS ADENOCARCINOMA             9              13
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    27   0   0   0
  FBXW7 WILD-TYPE 101   1  19   1
D6V9, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            27             101
  R1             0               1
  R2             0              19
  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"
D6V10, continuous

Clustering(7) Variable = SMAD2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED     6   3
  SMAD2 WILD-TYPE 109  23
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             132 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              3              23 
$`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 
       35.01        39.06        51.98 

$`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 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           4.01            0.92 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          53.00           54.02 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          35.01           21.50 
[1] "4.0 - 53.0 (35.0)" "0.9 - 54.0 (21.5)"
[1] "hr=" "1.5"
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD2 MUTATED         1        4         0         1         0          1
  SMAD2 WILD-TYPE      30       10        38         3        14          1
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED            0          0        2         0
  SMAD2 WILD-TYPE         12         16       19         1
D7V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                1              30
  STAGE II               4              10
  STAGE IIA              0              38
  STAGE IIB              1               3
  STAGE III              0              14
  STAGE IIIA             1               1
  STAGE IIIB             0              12
  STAGE IIIC             0              16
  STAGE IV               2              19
  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  3  5  2
  SMAD2 WILD-TYPE  4 30 97 13
D7V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               4
  T2             3              30
  T3             5              97
  T4             2              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
  SMAD2 MUTATED    7  2  1
  SMAD2 WILD-TYPE 83 28 33
D7V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             7              83
  N1             2              28
  N2             1              33
[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     7   2   0
  SMAD2 WILD-TYPE 123  19   1
D7V6, multiclass
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  M0              7             123
  M1              2              19
  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"
D7V7, binary
                 cls
clus               0  1
  SMAD2 MUTATED    3  7
  SMAD2 WILD-TYPE 74 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      3    7
  SMAD2 WILD-TYPE   74   70
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             3              74
  MALE               7              70
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     7   3
  SMAD2 WILD-TYPE 123  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      7    3
  SMAD2 WILD-TYPE  123   19
                               clus
vv                              SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             123
  COLON MUCINOUS ADENOCARCINOMA             3              19
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED     7   0   2   0
  SMAD2 WILD-TYPE 121   1  17   1
D7V9, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             7             121
  R1             0               1
  R2             2              17
  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"
D7V10, continuous

Clustering(8) Variable = BRAF MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    13   5
  BRAF WILD-TYPE 102  21
  BRAF MUTATED BRAF WILD-TYPE 
            18            123 
  BRAF MUTATED BRAF WILD-TYPE 
             5             21 
$`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 

$`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 
       40.96        16.31         0.95 

  BRAF MUTATED BRAF WILD-TYPE 
          0.99           0.92 
  BRAF MUTATED BRAF WILD-TYPE 
         54.02          53.00 
  BRAF MUTATED BRAF WILD-TYPE 
            17             24 
[1] "1.0 - 54.0 (17.0)" "0.9 - 53.0 (24.0)"
[1] "hr=" "1.9"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BRAF MUTATED         4        3         2         2         2          0
  BRAF WILD-TYPE      27       11        36         2        12          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED            4          2        1         0
  BRAF WILD-TYPE          8         14       20         1
D8V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               4             27
  STAGE II              3             11
  STAGE IIA             2             36
  STAGE IIB             2              2
  STAGE III             2             12
  STAGE IIIA            0              2
  STAGE IIIB            4              8
  STAGE IIIC            2             14
  STAGE IV              1             20
  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 11  5
  BRAF WILD-TYPE  3 30 91 10
D8V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            1              3
  T2            3             30
  T3           11             91
  T4            5             10
[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   11  5  4
  BRAF WILD-TYPE 79 25 30
D8V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           11             79
  N1            5             25
  N2            4             30
[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    19   1   0
  BRAF WILD-TYPE 111  20   1
D8V6, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  M0            19            111
  M1             1             20
  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"
D8V7, binary
                cls
clus              0  1
  BRAF MUTATED   14  6
  BRAF WILD-TYPE 63 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     14    6
  BRAF WILD-TYPE   63   71
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           14             63
  MALE              6             71
[1] 2 2
[1] FALSE
D8V8, binary
                cls
clus               0   1
  BRAF MUTATED    10  10
  BRAF WILD-TYPE 120  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10   10
  BRAF WILD-TYPE  120   12
                               clus
vv                              BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                    10            120
  COLON MUCINOUS ADENOCARCINOMA           10             12
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    17   0   1   0
  BRAF WILD-TYPE 111   1  18   1
D8V9, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           17            111
  R1            0              1
  R2            1             18
  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"
D8V10, continuous

Clustering(9) Variable = FAM123B MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  FAM123B MUTATED    10   5
  FAM123B WILD-TYPE 105  21
  FAM123B MUTATED FAM123B WILD-TYPE 
               15               126 
  FAM123B MUTATED FAM123B WILD-TYPE 
                5                21 
$`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 
       38.04        34.98         0.99 

$`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 

  FAM123B MUTATED FAM123B WILD-TYPE 
             0.99              0.92 
  FAM123B MUTATED FAM123B WILD-TYPE 
            53.00             54.02 
  FAM123B MUTATED FAM123B WILD-TYPE 
            19.07             23.69 
[1] "1.0 - 53.0 (19.1)" "0.9 - 54.0 (23.7)"
[1] "hr=" "2.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FAM123B MUTATED         2        2         7         1         2          0
  FAM123B WILD-TYPE      29       12        31         3        12          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM123B MUTATED            0          2        2         0
  FAM123B WILD-TYPE         12         14       19         1
D9V3, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  2                29
  STAGE II                 2                12
  STAGE IIA                7                31
  STAGE IIB                1                 3
  STAGE III                2                12
  STAGE IIIA               0                 2
  STAGE IIIB               0                12
  STAGE IIIC               2                14
  STAGE IV                 2                19
  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    0  3 13  3
  FAM123B WILD-TYPE  4 30 89 12
D9V4, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               0                 4
  T2               3                30
  T3              13                89
  T4               3                12
[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   13  1  5
  FAM123B WILD-TYPE 77 29 29
D9V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0              13                77
  N1               1                29
  N2               5                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
  FAM123B MUTATED    16   2   0
  FAM123B WILD-TYPE 114  19   1
D9V6, multiclass
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  M0               16               114
  M1                2                19
  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"
D9V7, binary
                   cls
clus                 0  1
  FAM123B MUTATED   10  9
  FAM123B WILD-TYPE 67 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     10    9
  FAM123B WILD-TYPE   67   68
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              10                67
  MALE                 9                68
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED    16   3
  FAM123B WILD-TYPE 114  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     16    3
  FAM123B WILD-TYPE  114   19
                               clus
vv                              FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                       16               114
  COLON MUCINOUS ADENOCARCINOMA               3                19
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    15   0   2   0
  FAM123B WILD-TYPE 113   1  17   1
D9V9, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              15               113
  R1               0                 1
  R2               2                17
  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"
D9V10, continuous

Clustering(10) Variable = MGC42105 MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                  0   1
  MGC42105 MUTATED     8   1
  MGC42105 WILD-TYPE 107  25
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                 9                132 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                 1                 25 
$`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 
        0.99        31.00        25.02 

$`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 

  MGC42105 MUTATED MGC42105 WILD-TYPE 
              0.99               0.92 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
             37.05              54.02 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
             26.99              22.50 
[1] "1.0 - 37.0 (27.0)" "0.9 - 54.0 (22.5)"
[1] "hr=" "1.7"
D10V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MGC42105 MUTATED         2        0         5         0         0          1
  MGC42105 WILD-TYPE      29       14        33         4        14          1
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGC42105 MUTATED            0          1        0         0
  MGC42105 WILD-TYPE         12         15       21         1
D10V3, multiclass
            clus
vv           MGC42105 MUTATED MGC42105 WILD-TYPE
  STAGE I                   2                 29
  STAGE II                  0                 14
  STAGE IIA                 5                 33
  STAGE IIB                 0                  4
  STAGE III                 0                 14
  STAGE IIIA                1                  1
  STAGE IIIB                0                 12
  STAGE IIIC                1                 15
  STAGE IV                  0                 21
  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  3  6  0
  MGC42105 WILD-TYPE  3 30 96 15
D10V4, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  T1                1                  3
  T2                3                 30
  T3                6                 96
  T4                0                 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
  MGC42105 MUTATED    8  1  1
  MGC42105 WILD-TYPE 82 29 33
D10V5, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  N0                8                 82
  N1                1                 29
  N2                1                 33
[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     9   0   0
  MGC42105 WILD-TYPE 121  21   1
D10V6, multiclass
     clus
vv    MGC42105 MUTATED MGC42105 WILD-TYPE
  M0                 9                121
  M1                 0                 21
  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"
D10V7, binary
                    cls
clus                  0  1
  MGC42105 MUTATED    6  4
  MGC42105 WILD-TYPE 71 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC42105 MUTATED      6    4
  MGC42105 WILD-TYPE   71   73
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  FEMALE                6                 71
  MALE                  4                 73
[1] 2 2
[1] FALSE
D10V8, binary
                    cls
clus                   0   1
  MGC42105 MUTATED     8   2
  MGC42105 WILD-TYPE 122  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC42105 MUTATED      8    2
  MGC42105 WILD-TYPE  122   20
                               clus
vv                              MGC42105 MUTATED MGC42105 WILD-TYPE
  COLON ADENOCARCINOMA                         8                122
  COLON MUCINOUS ADENOCARCINOMA                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  MGC42105 MUTATED     8   0   1   0
  MGC42105 WILD-TYPE 120   1  18   1
D10V9, multiclass
    clus
vv   MGC42105 MUTATED MGC42105 WILD-TYPE
  R0                8                120
  R1                0                  1
  R2                1                 18
  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"
D10V10, continuous

Clustering(11) Variable = ACVR1B MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED     9   3
  ACVR1B WILD-TYPE 106  23
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              12              129 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               3               23 
$`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 

$`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 
       40.96        16.31         0.95 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            0.99             0.92 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           51.98            54.02 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          22.535           23.380 
[1] "1.0 - 52.0 (22.5)" "0.9 - 54.0 (23.4)"
[1] "hr=" "1.4"
D11V2, continuous
                  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      30       11        36         3        12          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACVR1B MUTATED            2          1        1         0
  ACVR1B WILD-TYPE         10         15       20         1
D11V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1               30
  STAGE II                3               11
  STAGE IIA               2               36
  STAGE IIB               1                3
  STAGE III               2               12
  STAGE IIIA              0                2
  STAGE IIIB              2               10
  STAGE IIIC              1               15
  STAGE IV                1               20
  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  9  3
  ACVR1B WILD-TYPE  3 33 93 12
D11V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              1                3
  T2              0               33
  T3              9               93
  T4              3               12
[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  2  3
  ACVR1B WILD-TYPE 82 28 31
D11V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              8               82
  N1              2               28
  N2              3               31
[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    12   1   0
  ACVR1B WILD-TYPE 118  20   1
D11V6, multiclass
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  M0              12              118
  M1               1               20
  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"
D11V7, binary
                  cls
clus                0  1
  ACVR1B MUTATED    7  6
  ACVR1B WILD-TYPE 70 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      7    6
  ACVR1B WILD-TYPE   70   71
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              7               70
  MALE                6               71
[1] 2 2
[1] FALSE
D11V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     8   5
  ACVR1B WILD-TYPE 122  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      8    5
  ACVR1B WILD-TYPE  122   17
                               clus
vv                              ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON ADENOCARCINOMA                       8              122
  COLON MUCINOUS ADENOCARCINOMA              5               17
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED    12   0   1   0
  ACVR1B WILD-TYPE 116   1  18   1
D11V9, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             12              116
  R1              0                1
  R2              1               18
  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"
D11V10, continuous

Clustering(12) Variable = DNMT1 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  DNMT1 MUTATED     9   2
  DNMT1 WILD-TYPE 106  24
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             11             130 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
              2              24 
$`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 
       18.05         4.01        34.98         1.02        37.02 

$`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 
       18.05        40.96        16.31         0.95 

  DNMT1 MUTATED DNMT1 WILD-TYPE 
           0.92            0.92 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          37.02           54.02 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          18.05           23.69 
[1] "0.9 - 37.0 (18.1)" "0.9 - 54.0 (23.7)"
[1] "hr=" "1.2"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  DNMT1 MUTATED         1        2         4         2         1          0
  DNMT1 WILD-TYPE      30       12        34         2        13          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNMT1 MUTATED            1          0        1         0
  DNMT1 WILD-TYPE         11         16       20         1
D12V3, multiclass
            clus
vv           DNMT1 MUTATED DNMT1 WILD-TYPE
  STAGE I                1              30
  STAGE II               2              12
  STAGE IIA              4              34
  STAGE IIB              2               2
  STAGE III              1              13
  STAGE IIIA             0               2
  STAGE IIIB             1              11
  STAGE IIIC             0              16
  STAGE IV               1              20
  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  0  7  4
  DNMT1 WILD-TYPE  3 33 95 11
D12V4, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  T1             1               3
  T2             0              33
  T3             7              95
  T4             4              11
[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   10  2  0
  DNMT1 WILD-TYPE 80 28 34
D12V5, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  N0            10              80
  N1             2              28
  N2             0              34
[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    11   1   0
  DNMT1 WILD-TYPE 119  20   1
D12V6, multiclass
     clus
vv    DNMT1 MUTATED DNMT1 WILD-TYPE
  M0             11             119
  M1              1              20
  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"
D12V7, binary
                 cls
clus               0  1
  DNMT1 MUTATED    8  4
  DNMT1 WILD-TYPE 69 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED      8    4
  DNMT1 WILD-TYPE   69   73
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  FEMALE             8              69
  MALE               4              73
[1] 2 2
[1] FALSE
D12V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED     7   5
  DNMT1 WILD-TYPE 123  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED      7    5
  DNMT1 WILD-TYPE  123   17
                               clus
vv                              DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             123
  COLON MUCINOUS ADENOCARCINOMA             5              17
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNMT1 MUTATED    11   0   0   0
  DNMT1 WILD-TYPE 117   1  19   1
D12V9, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  R0            11             117
  R1             0               1
  R2             0              19
  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"
D12V10, continuous

Clustering(13) Variable = PCBP1 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  PCBP1 MUTATED     3   0
  PCBP1 WILD-TYPE 112  26
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              3             138 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              26 
$`PCBP1 MUTATED`
TCGA-AA-3941 TCGA-AA-3979 TCGA-AA-A01I 
          24           24           31 

$`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 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
          24.00            0.92 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          31.00           54.02 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
           24.0            22.5 
[1] "24.0 - 31.0 (24.0)" "0.9 - 54.0 (22.5)" 
[1] "hr="     "9300000"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCBP1 MUTATED         1        0         2         0         0          0
  PCBP1 WILD-TYPE      30       14        36         4        14          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED            0          0        0         1
  PCBP1 WILD-TYPE         12         16       21         0
D13V3, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                1              30
  STAGE II               0              14
  STAGE IIA              2              36
  STAGE IIB              0               4
  STAGE III              0              14
  STAGE IIIA             0               2
  STAGE IIIB             0              12
  STAGE IIIC             0              16
  STAGE IV               0              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
  PCBP1 MUTATED     0   1   2   1
  PCBP1 WILD-TYPE   4  32 100  14
D13V4, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               4
  T2             1              32
  T3             2             100
  T4             1              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
  PCBP1 MUTATED    3  1  0
  PCBP1 WILD-TYPE 87 29 34
D13V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0             3              87
  N1             1              29
  N2             0              34
[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     3   0   1
  PCBP1 WILD-TYPE 127  21   0
D13V6, multiclass
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  M0              3             127
  M1              0              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"
D13V7, binary
                 cls
clus               0  1
  PCBP1 MUTATED    2  2
  PCBP1 WILD-TYPE 75 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      2    2
  PCBP1 WILD-TYPE   75   75
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             2              75
  MALE               2              75
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     4   0
  PCBP1 WILD-TYPE 126  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      4    0
  PCBP1 WILD-TYPE  126   22
                               clus
vv                              PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             126
  COLON MUCINOUS ADENOCARCINOMA             0              22
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     4   0   0   0
  PCBP1 WILD-TYPE 124   1  19   1
D13V9, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             4             124
  R1             0               1
  R2             0              19
  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"
D13V10, continuous

Clustering(14) Variable = CDC27 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED     7   2
  CDC27 WILD-TYPE 108  24
  CDC27 MUTATED CDC27 WILD-TYPE 
              9             132 
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              24 
$`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 
       34.98        38.07         1.02 

$`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 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.99            0.92 
  CDC27 MUTATED CDC27 WILD-TYPE 
          38.07           54.02 
  CDC27 MUTATED CDC27 WILD-TYPE 
          18.05           23.69 
[1] "1.0 - 38.1 (18.1)" "0.9 - 54.0 (23.7)"
[1] "hr=" "1.6"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CDC27 MUTATED         1        1         5         1         2          0
  CDC27 WILD-TYPE      30       13        33         3        12          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC27 MUTATED            0          0        0         0
  CDC27 WILD-TYPE         12         16       21         1
D14V3, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                1              30
  STAGE II               1              13
  STAGE IIA              5              33
  STAGE IIB              1               3
  STAGE III              2              12
  STAGE IIIA             0               2
  STAGE IIIB             0              12
  STAGE IIIC             0              16
  STAGE IV               0              21
  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    0  1  8  1
  CDC27 WILD-TYPE  4 32 94 14
D14V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             0               4
  T2             1              32
  T3             8              94
  T4             1              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
  CDC27 MUTATED    8  1  1
  CDC27 WILD-TYPE 82 29 33
D14V5, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  N0             8              82
  N1             1              29
  N2             1              33
[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    10   0   0
  CDC27 WILD-TYPE 120  21   1
D14V6, multiclass
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  M0             10             120
  M1              0              21
  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"
D14V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    8  2
  CDC27 WILD-TYPE 69 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      8    2
  CDC27 WILD-TYPE   69   75
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             8              69
  MALE               2              75
[1] 2 2
[1] FALSE
D14V8, binary
                 cls
clus                0   1
  CDC27 MUTATED     9   1
  CDC27 WILD-TYPE 121  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      9    1
  CDC27 WILD-TYPE  121   21
                               clus
vv                              CDC27 MUTATED CDC27 WILD-TYPE
  COLON ADENOCARCINOMA                      9             121
  COLON MUCINOUS ADENOCARCINOMA             1              21
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDC27 MUTATED    10   0   0   0
  CDC27 WILD-TYPE 118   1  19   1
D14V9, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0            10             118
  R1             0               1
  R2             0              19
  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"
D14V10, continuous

Clustering(15) Variable = PIK3CA MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   18  6
  PIK3CA WILD-TYPE 97 20
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              24              117 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               6               20 
$`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 

$`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 
       41.00        16.31         0.95 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.92             0.92 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           53.00            54.02 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           31.00            21.01 
[1] "0.9 - 53.0 (31.0)" "0.9 - 54.0 (21.0)"
[1] "hr=" "1.4"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PIK3CA MUTATED         7        4         7         3         1          0
  PIK3CA WILD-TYPE      24       10        31         1        13          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIK3CA MUTATED            0          2        1         0
  PIK3CA WILD-TYPE         12         14       20         1
D15V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 7               24
  STAGE II                4               10
  STAGE IIA               7               31
  STAGE IIB               3                1
  STAGE III               1               13
  STAGE IIIA              0                2
  STAGE IIIB              0               12
  STAGE IIIC              2               14
  STAGE IV                1               20
  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  7 15  3
  PIK3CA WILD-TYPE  3 26 87 12
D15V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1                3
  T2              7               26
  T3             15               87
  T4              3               12
[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   22  1  3
  PIK3CA WILD-TYPE 68 29 31
D15V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             22               68
  N1              1               29
  N2              3               31
[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    24   1   0
  PIK3CA WILD-TYPE 106  20   1
D15V6, multiclass
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              24              106
  M1               1               20
  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"
D15V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED   12 14
  PIK3CA WILD-TYPE 65 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     12   14
  PIK3CA WILD-TYPE   65   63
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             12               65
  MALE               14               63
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    20   6
  PIK3CA WILD-TYPE 110  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20    6
  PIK3CA WILD-TYPE  110   16
                               clus
vv                              PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                      20              110
  COLON MUCINOUS ADENOCARCINOMA              6               16
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    24   0   1   0
  PIK3CA WILD-TYPE 104   1  18   1
D15V9, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             24              104
  R1              0                1
  R2              1               18
  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"
D15V10, continuous

Clustering(16) Variable = BCOR MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  BCOR MUTATED     3   2
  BCOR WILD-TYPE 112  24
  BCOR MUTATED BCOR WILD-TYPE 
             5            136 
  BCOR MUTATED BCOR WILD-TYPE 
             2             24 
$`BCOR MUTATED`
TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3930 TCGA-AA-A00N TCGA-AA-A010 
       29.95         0.92         2.01         4.01        34.98 

$`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 
       18.05        40.96        16.31         0.95 

  BCOR MUTATED BCOR WILD-TYPE 
          0.92           0.92 
  BCOR MUTATED BCOR WILD-TYPE 
         34.98          54.02 
  BCOR MUTATED BCOR WILD-TYPE 
          4.01          23.69 
[1] "0.9 - 35.0 (4.0)"  "0.9 - 54.0 (23.7)"
[1] "hr=" "3.7"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BCOR MUTATED         0        1         1         2         1          0
  BCOR WILD-TYPE      31       13        37         2        13          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED            0          0        1         0
  BCOR WILD-TYPE         12         16       20         1
D16V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               0             31
  STAGE II              1             13
  STAGE IIA             1             37
  STAGE IIB             2              2
  STAGE III             1             13
  STAGE IIIA            0              2
  STAGE IIIB            0             12
  STAGE IIIC            0             16
  STAGE IV              1             20
  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    0  0  3  3
  BCOR WILD-TYPE  4 33 99 12
D16V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0              4
  T2            0             33
  T3            3             99
  T4            3             12
[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    4  1  1
  BCOR WILD-TYPE 86 29 33
D16V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0            4             86
  N1            1             29
  N2            1             33
[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     5   1   0
  BCOR WILD-TYPE 125  20   1
D16V6, multiclass
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  M0             5            125
  M1             1             20
  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"
D16V7, binary
                cls
clus              0  1
  BCOR MUTATED    4  2
  BCOR WILD-TYPE 73 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      4    2
  BCOR WILD-TYPE   73   75
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE            4             73
  MALE              2             75
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus               0   1
  BCOR MUTATED     4   2
  BCOR WILD-TYPE 126  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      4    2
  BCOR WILD-TYPE  126   20
                               clus
vv                              BCOR MUTATED BCOR WILD-TYPE
  COLON ADENOCARCINOMA                     4            126
  COLON MUCINOUS ADENOCARCINOMA            2             20
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED     5   0   1   0
  BCOR WILD-TYPE 123   1  18   1
D16V9, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0            5            123
  R1            0              1
  R2            1             18
  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"
D16V10, continuous

Clustering(17) Variable = ZHX2 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  ZHX2 MUTATED     7   0
  ZHX2 WILD-TYPE 108  26
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             7            134 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             0             26 
$`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 
       34.98 

$`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 
       16.31         0.95 

  ZHX2 MUTATED ZHX2 WILD-TYPE 
          0.99           0.92 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         46.65          54.02 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         26.01          21.50 
[1] "1.0 - 46.6 (26.0)" "0.9 - 54.0 (21.5)"
[1] "hr="     "2.7e+07"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ZHX2 MUTATED         1        1         2         1         0          1
  ZHX2 WILD-TYPE      30       13        36         3        14          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX2 MUTATED            1          0        0         0
  ZHX2 WILD-TYPE         11         16       21         1
D17V3, multiclass
            clus
vv           ZHX2 MUTATED ZHX2 WILD-TYPE
  STAGE I               1             30
  STAGE II              1             13
  STAGE IIA             2             36
  STAGE IIB             1              3
  STAGE III             0             14
  STAGE IIIA            1              1
  STAGE IIIB            1             11
  STAGE IIIC            0             16
  STAGE IV              0             21
  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  3  3  2
  ZHX2 WILD-TYPE  4 30 99 13
D17V4, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  T1            0              4
  T2            3             30
  T3            3             99
  T4            2             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
  ZHX2 MUTATED    6  2  0
  ZHX2 WILD-TYPE 84 28 34
D17V5, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  N0            6             84
  N1            2             28
  N2            0             34
[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     7   0   0
  ZHX2 WILD-TYPE 123  21   1
D17V6, multiclass
     clus
vv    ZHX2 MUTATED ZHX2 WILD-TYPE
  M0             7            123
  M1             0             21
  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"
D17V7, binary
                cls
clus              0  1
  ZHX2 MUTATED    4  4
  ZHX2 WILD-TYPE 73 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      4    4
  ZHX2 WILD-TYPE   73   73
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  FEMALE            4             73
  MALE              4             73
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus               0   1
  ZHX2 MUTATED     8   0
  ZHX2 WILD-TYPE 122  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      8    0
  ZHX2 WILD-TYPE  122   22
                               clus
vv                              ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            122
  COLON MUCINOUS ADENOCARCINOMA            0             22
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZHX2 MUTATED     7   0   0   0
  ZHX2 WILD-TYPE 121   1  19   1
D17V9, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  R0            7            121
  R1            0              1
  R2            0             19
  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"
D17V10, continuous

Clustering(18) Variable = KLHL5 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  KLHL5 MUTATED     3   1
  KLHL5 WILD-TYPE 112  25
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              4             137 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              1              25 
$`KLHL5 MUTATED`
TCGA-AA-3672 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 
        0.92        20.98         4.01        34.98 

$`KLHL5 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-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-3956 
       12.99        24.00        33.01        26.01         2.01        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-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-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 
       39.98        18.05        40.96        16.31         0.95 

  KLHL5 MUTATED KLHL5 WILD-TYPE 
           0.92            0.92 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
          34.98           54.02 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
         12.495          24.000 
[1] "0.9 - 35.0 (12.5)" "0.9 - 54.0 (24.0)"
[1] "hr=" "2.1"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KLHL5 MUTATED         0        0         1         2         1          0
  KLHL5 WILD-TYPE      31       14        37         2        13          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLHL5 MUTATED            1          0        0         0
  KLHL5 WILD-TYPE         11         16       21         1
D18V3, multiclass
            clus
vv           KLHL5 MUTATED KLHL5 WILD-TYPE
  STAGE I                0              31
  STAGE II               0              14
  STAGE IIA              1              37
  STAGE IIB              2               2
  STAGE III              1              13
  STAGE IIIA             0               2
  STAGE IIIB             1              11
  STAGE IIIC             0              16
  STAGE IV               0              21
  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
  KLHL5 MUTATED     0   1   2   2
  KLHL5 WILD-TYPE   4  32 100  13
D18V4, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  T1             0               4
  T2             1              32
  T3             2             100
  T4             2              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
  KLHL5 MUTATED    3  1  1
  KLHL5 WILD-TYPE 87 29 33
D18V5, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  N0             3              87
  N1             1              29
  N2             1              33
[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
  KLHL5 MUTATED     5   0   0
  KLHL5 WILD-TYPE 125  21   1
D18V6, multiclass
     clus
vv    KLHL5 MUTATED KLHL5 WILD-TYPE
  M0              5             125
  M1              0              21
  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"
D18V7, binary
                 cls
clus               0  1
  KLHL5 MUTATED    3  2
  KLHL5 WILD-TYPE 74 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      3    2
  KLHL5 WILD-TYPE   74   75
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  FEMALE             3              74
  MALE               2              75
[1] 2 2
[1] FALSE
D18V8, binary
                 cls
clus                0   1
  KLHL5 MUTATED     4   1
  KLHL5 WILD-TYPE 126  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      4    1
  KLHL5 WILD-TYPE  126   21
                               clus
vv                              KLHL5 MUTATED KLHL5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             126
  COLON MUCINOUS ADENOCARCINOMA             1              21
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLHL5 MUTATED     5   0   0   0
  KLHL5 WILD-TYPE 123   1  19   1
D18V9, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  R0             5             123
  R1             0               1
  R2             0              19
  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"
D18V10, continuous

Clustering(19) Variable = CASP8 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     8   1
  CASP8 WILD-TYPE 107  25
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             132 
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              25 
$`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 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.99            0.92 
  CASP8 MUTATED CASP8 WILD-TYPE 
          53.00           54.02 
  CASP8 MUTATED CASP8 WILD-TYPE 
          18.05           23.69 
[1] "1.0 - 53.0 (18.1)" "0.9 - 54.0 (23.7)"
[1] "hr=" "1.4"
D19V2, continuous
                 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      29       11        35         3        14          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED            1          0        0         0
  CASP8 WILD-TYPE         11         16       21         1
D19V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                2              29
  STAGE II               3              11
  STAGE IIA              3              35
  STAGE IIB              1               3
  STAGE III              0              14
  STAGE IIIA             0               2
  STAGE IIIB             1              11
  STAGE IIIC             0              16
  STAGE IV               0              21
  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  4 31 97 12
D19V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             0               4
  T2             2              31
  T3             5              97
  T4             3              12
[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 81 29 34
D19V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             9              81
  N1             1              29
  N2             0              34
[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 120  21   1
D19V6, multiclass
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  M0             10             120
  M1              0              21
  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"
D19V7, binary
                 cls
clus               0  1
  CASP8 MUTATED    5  5
  CASP8 WILD-TYPE 72 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    5
  CASP8 WILD-TYPE   72   72
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             5              72
  MALE               5              72
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     7   3
  CASP8 WILD-TYPE 123  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      7    3
  CASP8 WILD-TYPE  123   19
                               clus
vv                              CASP8 MUTATED CASP8 WILD-TYPE
  COLON ADENOCARCINOMA                      7             123
  COLON MUCINOUS ADENOCARCINOMA             3              19
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    10   0   0   0
  CASP8 WILD-TYPE 118   1  19   1
D19V9, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            10             118
  R1             0               1
  R2             0              19
  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"
D19V10, continuous

Clustering(20) Variable = PCDHGB1 MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  PCDHGB1 MUTATED     4   2
  PCDHGB1 WILD-TYPE 111  24
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                6               135 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                2                24 
$`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 

$`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 
       40.96        16.31         0.95 

  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
             0.92              0.92 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
            53.00             54.02 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
             3.01             24.00 
[1] "0.9 - 53.0 (3.0)"  "0.9 - 54.0 (24.0)"
[1] "hr=" "2.7"
D20V2, continuous
                   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      31       13        36         2        13          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGB1 MUTATED            0          1        0         0
  PCDHGB1 WILD-TYPE         12         15       21         1
D20V3, multiclass
            clus
vv           PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  STAGE I                  0                31
  STAGE II                 1                13
  STAGE IIA                2                36
  STAGE IIB                2                 2
  STAGE III                1                13
  STAGE IIIA               0                 2
  STAGE IIIB               0                12
  STAGE IIIC               1                15
  STAGE IV                 0                21
  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  5  2
  PCDHGB1 WILD-TYPE  4 33 97 13
D20V4, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  T1               0                 4
  T2               0                33
  T3               5                97
  T4               2                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
  PCDHGB1 MUTATED    5  1  1
  PCDHGB1 WILD-TYPE 85 29 33
D20V5, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  N0               5                85
  N1               1                29
  N2               1                33
[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     7   0   0
  PCDHGB1 WILD-TYPE 123  21   1
D20V6, multiclass
     clus
vv    PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  M0                7               123
  M1                0                21
  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"
D20V7, binary
                   cls
clus                 0  1
  PCDHGB1 MUTATED    5  2
  PCDHGB1 WILD-TYPE 72 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB1 MUTATED      5    2
  PCDHGB1 WILD-TYPE   72   75
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  FEMALE               5                72
  MALE                 2                75
[1] 2 2
[1] FALSE
D20V8, binary
                   cls
clus                  0   1
  PCDHGB1 MUTATED     5   2
  PCDHGB1 WILD-TYPE 125  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB1 MUTATED      5    2
  PCDHGB1 WILD-TYPE  125   20
                               clus
vv                              PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               125
  COLON MUCINOUS ADENOCARCINOMA               2                20
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGB1 MUTATED     6   0   0   0
  PCDHGB1 WILD-TYPE 122   1  19   1
D20V9, multiclass
    clus
vv   PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  R0               6               122
  R1               0                 1
  R2               0                19
  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"
D20V10, continuous

Clustering(21) Variable = UBXN11 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  UBXN11 MUTATED     3   0
  UBXN11 WILD-TYPE 112  26
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               3              138 
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               0               26 
$`UBXN11 MUTATED`
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A01R 
       31.00        33.01        35.01 

$`UBXN11 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-3930 
       17.03        24.03        27.02        29.98        18.05         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-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-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-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 

  UBXN11 MUTATED UBXN11 WILD-TYPE 
           31.00             0.92 
  UBXN11 MUTATED UBXN11 WILD-TYPE 
           35.01            54.02 
  UBXN11 MUTATED UBXN11 WILD-TYPE 
           33.01            22.50 
[1] "31.0 - 35.0 (33.0)" "0.9 - 54.0 (22.5)" 
[1] "hr="     "2.5e+07"
D21V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  UBXN11 MUTATED         1        0         0         1         1          0
  UBXN11 WILD-TYPE      30       14        38         3        13          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBXN11 MUTATED            0          0        0         0
  UBXN11 WILD-TYPE         12         16       21         1
D21V3, multiclass
            clus
vv           UBXN11 MUTATED UBXN11 WILD-TYPE
  STAGE I                 1               30
  STAGE II                0               14
  STAGE IIA               0               38
  STAGE IIB               1                3
  STAGE III               1               13
  STAGE IIIA              0                2
  STAGE IIIB              0               12
  STAGE IIIC              0               16
  STAGE IV                0               21
  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
  UBXN11 MUTATED     1   0   1   1
  UBXN11 WILD-TYPE   3  33 101  14
D21V4, multiclass
    clus
vv   UBXN11 MUTATED UBXN11 WILD-TYPE
  T1              1                3
  T2              0               33
  T3              1              101
  T4              1               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
  UBXN11 MUTATED    2  0  1
  UBXN11 WILD-TYPE 88 30 33
D21V5, multiclass
    clus
vv   UBXN11 MUTATED UBXN11 WILD-TYPE
  N0              2               88
  N1              0               30
  N2              1               33
[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
  UBXN11 MUTATED     3   0   0
  UBXN11 WILD-TYPE 127  21   1
D21V6, multiclass
     clus
vv    UBXN11 MUTATED UBXN11 WILD-TYPE
  M0               3              127
  M1               0               21
  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"
D21V7, binary
                  cls
clus                0  1
  UBXN11 MUTATED    2  1
  UBXN11 WILD-TYPE 75 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBXN11 MUTATED      2    1
  UBXN11 WILD-TYPE   75   76
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  FEMALE              2               75
  MALE                1               76
[1] 2 2
[1] FALSE
D21V8, binary
                  cls
clus                 0   1
  UBXN11 MUTATED     0   3
  UBXN11 WILD-TYPE 130  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBXN11 MUTATED      0    3
  UBXN11 WILD-TYPE  130   19
                               clus
vv                              UBXN11 MUTATED UBXN11 WILD-TYPE
  COLON ADENOCARCINOMA                       0              130
  COLON MUCINOUS ADENOCARCINOMA              3               19
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UBXN11 MUTATED     3   0   0   0
  UBXN11 WILD-TYPE 125   1  19   1
D21V9, multiclass
    clus
vv   UBXN11 MUTATED UBXN11 WILD-TYPE
  R0              3              125
  R1              0                1
  R2              0               19
  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"
D21V10, continuous

Clustering(22) Variable = MIER3 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  MIER3 MUTATED     7   1
  MIER3 WILD-TYPE 108  25
  MIER3 MUTATED MIER3 WILD-TYPE 
              8             133 
  MIER3 MUTATED MIER3 WILD-TYPE 
              1              25 
$`MIER3 MUTATED`
TCGA-A6-2672 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3864 
       46.65        19.07        29.95         0.92         0.99        53.00 
TCGA-AA-3977 TCGA-AA-A010 
       25.02        34.98 

$`MIER3 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-3530 
        9.07        24.03        37.05        36.03         8.05        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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        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-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-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-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        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-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-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-A01V TCGA-AA-A01X 
        1.02        35.01         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 
        0.95 

  MIER3 MUTATED MIER3 WILD-TYPE 
           0.92            0.92 
  MIER3 MUTATED MIER3 WILD-TYPE 
          53.00           54.02 
  MIER3 MUTATED MIER3 WILD-TYPE 
         27.485          23.010 
[1] "0.9 - 53.0 (27.5)" "0.9 - 54.0 (23.0)"
[1] "hr=" "1.6"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MIER3 MUTATED         1        3         2         1         1          0
  MIER3 WILD-TYPE      30       11        36         3        13          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIER3 MUTATED            1          0        0         0
  MIER3 WILD-TYPE         11         16       21         1
D22V3, multiclass
            clus
vv           MIER3 MUTATED MIER3 WILD-TYPE
  STAGE I                1              30
  STAGE II               3              11
  STAGE IIA              2              36
  STAGE IIB              1               3
  STAGE III              1              13
  STAGE IIIA             0               2
  STAGE IIIB             1              11
  STAGE IIIC             0              16
  STAGE IV               0              21
  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
  MIER3 MUTATED    0  2  6  2
  MIER3 WILD-TYPE  4 31 96 13
D22V4, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  T1             0               4
  T2             2              31
  T3             6              96
  T4             2              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
  MIER3 MUTATED    8  2  0
  MIER3 WILD-TYPE 82 28 34
D22V5, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  N0             8              82
  N1             2              28
  N2             0              34
[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
  MIER3 MUTATED     9   0   0
  MIER3 WILD-TYPE 121  21   1
D22V6, multiclass
     clus
vv    MIER3 MUTATED MIER3 WILD-TYPE
  M0              9             121
  M1              0              21
  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"
D22V7, binary
                 cls
clus               0  1
  MIER3 MUTATED    6  4
  MIER3 WILD-TYPE 71 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED      6    4
  MIER3 WILD-TYPE   71   73
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  FEMALE             6              71
  MALE               4              73
[1] 2 2
[1] FALSE
D22V8, binary
                 cls
clus                0   1
  MIER3 MUTATED     9   1
  MIER3 WILD-TYPE 121  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED      9    1
  MIER3 WILD-TYPE  121   21
                               clus
vv                              MIER3 MUTATED MIER3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             121
  COLON MUCINOUS ADENOCARCINOMA             1              21
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MIER3 MUTATED     9   0   0   0
  MIER3 WILD-TYPE 119   1  19   1
D22V9, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  R0             9             119
  R1             0               1
  R2             0              19
  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"
D22V10, continuous

Clustering(23) Variable = TBC1D10C MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     3   0
  TBC1D10C WILD-TYPE 112  26
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                138 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 0                 26 
$`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 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.02               0.92 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             26.01              54.02 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             16.08              23.69 
[1] "1.0 - 26.0 (16.1)" "0.9 - 54.0 (23.7)"
[1] "hr="     "9100000"
D23V2, continuous
                    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      30       14        38         4        13          2
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBC1D10C MUTATED            1          0        0         0
  TBC1D10C WILD-TYPE         11         16       21         1
D23V3, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                 30
  STAGE II                  0                 14
  STAGE IIA                 0                 38
  STAGE IIB                 0                  4
  STAGE III                 1                 13
  STAGE IIIA                0                  2
  STAGE IIIB                1                 11
  STAGE IIIC                0                 16
  STAGE IV                  0                 21
  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   4  32 100  15
D23V4, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                0                  4
  T2                1                 32
  T3                2                100
  T4                0                 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
  TBC1D10C MUTATED    1  2  0
  TBC1D10C WILD-TYPE 89 28 34
D23V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                1                 89
  N1                2                 28
  N2                0                 34
[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 127  21   1
D23V6, multiclass
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  M0                 3                127
  M1                 0                 21
  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"
D23V7, binary
                    cls
clus                  0  1
  TBC1D10C MUTATED    2  1
  TBC1D10C WILD-TYPE 75 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      2    1
  TBC1D10C WILD-TYPE   75   76
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                2                 75
  MALE                  1                 76
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     1   2
  TBC1D10C WILD-TYPE 129  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      1    2
  TBC1D10C WILD-TYPE  129   20
                               clus
vv                              TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON ADENOCARCINOMA                         1                129
  COLON MUCINOUS ADENOCARCINOMA                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TBC1D10C MUTATED     3   0   0   0
  TBC1D10C WILD-TYPE 125   1  19   1
D23V9, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                3                125
  R1                0                  1
  R2                0                 19
  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"
D23V10, continuous

Clustering(24) Variable = TCF7L2 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  TCF7L2 MUTATED     8   0
  TCF7L2 WILD-TYPE 107  26
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               8              133 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               0               26 
$`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 
       31.00        33.04 

$`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 
        0.95 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.92             0.92 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           50.04            54.02 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           28.01            23.01 
[1] "0.9 - 50.0 (28.0)" "0.9 - 54.0 (23.0)"
[1] "hr="     "2.7e+07"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TCF7L2 MUTATED         1        2         2         1         2          0
  TCF7L2 WILD-TYPE      30       12        36         3        12          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7L2 MUTATED            1          0        1         0
  TCF7L2 WILD-TYPE         11         16       20         1
D24V3, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 1               30
  STAGE II                2               12
  STAGE IIA               2               36
  STAGE IIB               1                3
  STAGE III               2               12
  STAGE IIIA              0                2
  STAGE IIIB              1               11
  STAGE IIIC              0               16
  STAGE IV                1               20
  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  3  6  2
  TCF7L2 WILD-TYPE  4 30 96 13
D24V4, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                4
  T2              3               30
  T3              6               96
  T4              2               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
  TCF7L2 MUTATED    7  2  2
  TCF7L2 WILD-TYPE 83 28 32
D24V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0              7               83
  N1              2               28
  N2              2               32
[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     9   1   0
  TCF7L2 WILD-TYPE 121  20   1
D24V6, multiclass
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  M0               9              121
  M1               1               20
  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"
D24V7, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    7  4
  TCF7L2 WILD-TYPE 70 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      7    4
  TCF7L2 WILD-TYPE   70   73
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE              7               70
  MALE                4               73
[1] 2 2
[1] FALSE
D24V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    11   0
  TCF7L2 WILD-TYPE 119  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     11    0
  TCF7L2 WILD-TYPE  119   22
                               clus
vv                              TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              119
  COLON MUCINOUS ADENOCARCINOMA              0               22
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCF7L2 MUTATED     9   0   1   0
  TCF7L2 WILD-TYPE 119   1  18   1
D24V9, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0              9              119
  R1              0                1
  R2              1               18
  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"
D24V10, continuous

Clustering(25) Variable = PCDHGA9 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  PCDHGA9 MUTATED     4   1
  PCDHGA9 WILD-TYPE 111  25
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                5               136 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                1                25 
$`PCDHGA9 MUTATED`
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3877 TCGA-AY-4070 
       54.02         0.92        53.00        31.00        16.31 

$`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 
       39.98        18.05        40.96         0.95 

  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
             0.92              0.92 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
            54.02             51.98 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
           31.000            23.195 
[1] "0.9 - 54.0 (31.0)" "0.9 - 52.0 (23.2)"
[1] "hr=" "1.1"
D25V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCDHGA9 MUTATED         1        2         0         0         1          0
  PCDHGA9 WILD-TYPE      30       12        38         4        13          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGA9 MUTATED            0          1        0         0
  PCDHGA9 WILD-TYPE         12         15       21         1
D25V3, multiclass
            clus
vv           PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  STAGE I                  1                30
  STAGE II                 2                12
  STAGE IIA                0                38
  STAGE IIB                0                 4
  STAGE III                1                13
  STAGE IIIA               0                 2
  STAGE IIIB               0                12
  STAGE IIIC               1                15
  STAGE IV                 0                21
  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  0  4  0
  PCDHGA9 WILD-TYPE  3 33 98 15
D25V4, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  T1               1                 3
  T2               0                33
  T3               4                98
  T4               0                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
  PCDHGA9 MUTATED    3  1  1
  PCDHGA9 WILD-TYPE 87 29 33
D25V5, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  N0               3                87
  N1               1                29
  N2               1                33
[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     5   0   0
  PCDHGA9 WILD-TYPE 125  21   1
D25V6, multiclass
     clus
vv    PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  M0                5               125
  M1                0                21
  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"
D25V7, binary
                   cls
clus                 0  1
  PCDHGA9 MUTATED    4  1
  PCDHGA9 WILD-TYPE 73 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      4    1
  PCDHGA9 WILD-TYPE   73   76
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  FEMALE               4                73
  MALE                 1                76
[1] 2 2
[1] FALSE
D25V8, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     4   1
  PCDHGA9 WILD-TYPE 126  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      4    1
  PCDHGA9 WILD-TYPE  126   21
                               clus
vv                              PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  COLON ADENOCARCINOMA                        4               126
  COLON MUCINOUS ADENOCARCINOMA               1                21
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGA9 MUTATED     4   1   0   0
  PCDHGA9 WILD-TYPE 124   0  19   1
D25V9, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  R0               4               124
  R1               1                 0
  R2               0                19
  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"
D25V10, continuous

Clustering(26) Variable = PCDHGA7 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  PCDHGA7 MUTATED     3   1
  PCDHGA7 WILD-TYPE 112  25
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                4               137 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                1                25 
$`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 
       39.98        18.05        40.96        16.31         0.95 

  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
             4.01              0.92 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
            47.01             54.02 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
           25.005            23.010 
[1] "4.0 - 47.0 (25.0)" "0.9 - 54.0 (23.0)"
[1] "hr=" "1.2"
D26V2, continuous
                   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      31       14        36         3        13          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDHGA7 MUTATED            1          0        0         0
  PCDHGA7 WILD-TYPE         11         16       21         1
D26V3, multiclass
            clus
vv           PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  STAGE I                  0                31
  STAGE II                 0                14
  STAGE IIA                2                36
  STAGE IIB                1                 3
  STAGE III                1                13
  STAGE IIIA               0                 2
  STAGE IIIB               1                11
  STAGE IIIC               0                16
  STAGE IV                 0                21
  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  4 32 99 14
D26V4, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  T1               0                 4
  T2               1                32
  T3               3                99
  T4               1                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
  PCDHGA7 MUTATED    3  2  0
  PCDHGA7 WILD-TYPE 87 28 34
D26V5, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  N0               3                87
  N1               2                28
  N2               0                34
[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 125  21   1
D26V6, multiclass
     clus
vv    PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  M0                5               125
  M1                0                21
  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"
D26V7, binary
                   cls
clus                 0  1
  PCDHGA7 MUTATED    3  2
  PCDHGA7 WILD-TYPE 74 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA7 MUTATED      3    2
  PCDHGA7 WILD-TYPE   74   75
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  FEMALE               3                74
  MALE                 2                75
[1] 2 2
[1] FALSE
D26V8, binary
                   cls
clus                  0   1
  PCDHGA7 MUTATED     3   2
  PCDHGA7 WILD-TYPE 127  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA7 MUTATED      3    2
  PCDHGA7 WILD-TYPE  127   20
                               clus
vv                              PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  COLON ADENOCARCINOMA                        3               127
  COLON MUCINOUS ADENOCARCINOMA               2                20
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGA7 MUTATED     5   0   0   0
  PCDHGA7 WILD-TYPE 123   1  19   1
D26V9, multiclass
    clus
vv   PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  R0               5               123
  R1               0                 1
  R2               0                19
  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"
D26V10, continuous

Clustering(27) Variable = KLK2 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  KLK2 MUTATED     3   0
  KLK2 WILD-TYPE 112  26
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            138 
  KLK2 MUTATED KLK2 WILD-TYPE 
             0             26 
$`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 

  KLK2 MUTATED KLK2 WILD-TYPE 
         12.99           0.92 
  KLK2 MUTATED KLK2 WILD-TYPE 
         38.04          54.02 
  KLK2 MUTATED KLK2 WILD-TYPE 
        29.950         23.195 
[1] "13.0 - 38.0 (29.9)" "0.9 - 54.0 (23.2)" 
[1] "hr="     "9200000"
D27V2, continuous
                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      31       14        36         4        14          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLK2 MUTATED            0          1        0         0
  KLK2 WILD-TYPE         12         15       21         1
D27V3, multiclass
            clus
vv           KLK2 MUTATED KLK2 WILD-TYPE
  STAGE I               0             31
  STAGE II              0             14
  STAGE IIA             2             36
  STAGE IIB             0              4
  STAGE III             0             14
  STAGE IIIA            0              2
  STAGE IIIB            0             12
  STAGE IIIC            1             15
  STAGE IV              0             21
  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  4 33 99 15
D27V4, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  T1            0              4
  T2            0             33
  T3            3             99
  T4            0             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
  KLK2 MUTATED    2  0  1
  KLK2 WILD-TYPE 88 30 33
D27V5, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  N0            2             88
  N1            0             30
  N2            1             33
[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 127  21   1
D27V6, multiclass
     clus
vv    KLK2 MUTATED KLK2 WILD-TYPE
  M0             3            127
  M1             0             21
  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"
D27V7, binary
                cls
clus              0  1
  KLK2 MUTATED    1  2
  KLK2 WILD-TYPE 76 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK2 MUTATED      1    2
  KLK2 WILD-TYPE   76   75
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  FEMALE            1             76
  MALE              2             75
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus               0   1
  KLK2 MUTATED     2   1
  KLK2 WILD-TYPE 128  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK2 MUTATED      2    1
  KLK2 WILD-TYPE  128   21
                               clus
vv                              KLK2 MUTATED KLK2 WILD-TYPE
  COLON ADENOCARCINOMA                     2            128
  COLON MUCINOUS ADENOCARCINOMA            1             21
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLK2 MUTATED     3   0   0   0
  KLK2 WILD-TYPE 125   1  19   1
D27V9, multiclass
    clus
vv   KLK2 MUTATED KLK2 WILD-TYPE
  R0            3            125
  R1            0              1
  R2            0             19
  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"
D27V10, continuous
