[1] "ofn"        "-oTREAD-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/READ-TP/22507018/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/22571878/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=122, common to both=122
[1]  40 122
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          108            14 
  APC MUTATED APC WILD-TYPE 
          108            14 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              111 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              111 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            91             31 
  TP53 MUTATED TP53 WILD-TYPE 
            91             31 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            11            111 
  NRAS MUTATED NRAS WILD-TYPE 
            11            111 
[1] "FMN2 MUTATION ANALYSIS"
[1] 3
  FMN2 MUTATED FMN2 WILD-TYPE 
            14            108 
  FMN2 MUTATED FMN2 WILD-TYPE 
            14            108 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               115 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               115 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             5            117 
  RPTN MUTATED RPTN WILD-TYPE 
             5            117 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            110 
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            110 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              6             116 
  RBM10 MUTATED RBM10 WILD-TYPE 
              6             116 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              5             117 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              5             117 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
[1] "GABRP MUTATION ANALYSIS"
[1] 3
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
             4            118 
  RLIM MUTATED RLIM WILD-TYPE 
             4            118 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              6             116 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              6             116 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              12              110 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              12              110 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             117 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             117 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            63             59 
  KRAS MUTATED KRAS WILD-TYPE 
            63             59 
[1] "FLT1 MUTATION ANALYSIS"
[1] 3
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
[1] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
[1] "AKAP9 MUTATION ANALYSIS"
[1] 3
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              7             115 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              7             115 
[1] "VCX2 MUTATION ANALYSIS"
[1] 3
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            117 
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            117 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            118 
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            118 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              36               86 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              36               86 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            13            109 
  BRAF MUTATED BRAF WILD-TYPE 
            13            109 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             113 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             113 
[1] "CDKL5 MUTATION ANALYSIS"
[1] 3
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              4             118 
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              4             118 
[1] "ZNF354C MUTATION ANALYSIS"
[1] 3
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
[1] "IQCD MUTATION ANALYSIS"
[1] 3
  IQCD MUTATED IQCD WILD-TYPE 
             3            119 
  IQCD MUTATED IQCD WILD-TYPE 
             3            119 
[1] "ZBED4 MUTATION ANALYSIS"
[1] 3
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              4             118 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              4             118 
[1] "GMCL1 MUTATION ANALYSIS"
[1] 3
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              4             118 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              4             118 
[1] "CIR1 MUTATION ANALYSIS"
[1] 3
  CIR1 MUTATED CIR1 WILD-TYPE 
             3            119 
  CIR1 MUTATED CIR1 WILD-TYPE 
             3            119 
[1] "AGL MUTATION ANALYSIS"
[1] 3
  AGL MUTATED AGL WILD-TYPE 
            4           118 
  AGL MUTATED AGL WILD-TYPE 
            4           118 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               10               112 
  FAM123B MUTATED FAM123B WILD-TYPE 
               10               112 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              10              112 
  CREBBP MUTATED CREBBP WILD-TYPE 
              10              112 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 122 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=77,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 122 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES"
YEARS_TO_BIRTH, nv=39, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
 8 25 80  9 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 8 25 80  9 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 8 25 80  9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 8 25 80  9 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
67 32 21 
[1] "table(vv)"
vv
N0 N1 N2 
67 32 21 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
67 32 21 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
67 32 21 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, 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   84 18
  APC WILD-TYPE 11  3
  APC MUTATED APC WILD-TYPE 
          102            14 
  APC MUTATED APC WILD-TYPE 
           18             3 
$`APC MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A014 
       10.39         8.02        13.94        19.99        17.03        15.95 
TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       36.03        55.76        26.43        46.92        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       24.59         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 
       34.03         2.01        50.04        12.03         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        6.02        37.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         2.50 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       17.49        43.20        27.55         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       44.78        48.20        78.12         7.17        26.04        31.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         3.48        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 

$`APC WILD-TYPE`
TCGA-AG-4008 TCGA-AG-A00H TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       17.03        25.97        39.48        36.03        12.00        32.02 
TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3901 TCGA-AG-A00Y TCGA-AG-A016 
       36.03         6.05        15.95        25.02        23.01         9.07 
TCGA-DT-5265 TCGA-EI-6507 
       12.62        19.96 

  APC MUTATED APC WILD-TYPE 
         0.99          6.05 
  APC MUTATED APC WILD-TYPE 
       126.44         39.48 
  APC MUTATED APC WILD-TYPE 
       24.475        21.485 
[1] "1.0 - 126.4 (24.5)" "6.0 - 39.5 (21.5)" 
[1] "hr=" "1.9"
D1V2, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  APC MUTATED        27        4        23         2         4          4
  APC WILD-TYPE       0        3         6         0         0          0
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED           15          9       10         5
  APC WILD-TYPE          1          1        3         0
D1V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             27             0
  STAGE II             4             3
  STAGE IIA           23             6
  STAGE IIB            2             0
  STAGE III            4             0
  STAGE IIIA           4             0
  STAGE IIIB          15             1
  STAGE IIIC           9             1
  STAGE IV            10             3
  STAGE IVA            5             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    8 25 66  9
  APC WILD-TYPE  0  0 14  0
D1V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           8             0
  T2          25             0
  T3          66            14
  T4           9             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"
               vv
clus            N0 N1 N2
  APC MUTATED   58 30 18
  APC WILD-TYPE  9  2  3
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          58             9
  N1          30             2
  N2          18             3
[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"
D1V6, binary
               cls
clus             0  1
  APC MUTATED   81 14
  APC WILD-TYPE 11  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     81   14
  APC WILD-TYPE   11    3
   clus
vv  APC MUTATED APC WILD-TYPE
  0          81            11
  1          14             3
[1] 2 2
[1] FALSE
D1V7, binary
               cls
clus             0  1
  APC MUTATED   50 58
  APC WILD-TYPE  5  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     50   58
  APC WILD-TYPE    5    9
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          50             5
  MALE            58             9
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus             0  1
  APC MUTATED   66 13
  APC WILD-TYPE 11  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     66   13
  APC WILD-TYPE   11    3
     clus
vv    APC MUTATED APC WILD-TYPE
  NO           66            11
  YES          13             3
[1] 2 2
[1] FALSE
D1V9, binary
               cls
clus             0  1
  APC MUTATED   95  7
  APC WILD-TYPE 11  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     95    7
  APC WILD-TYPE   11    3
                                clus
vv                               APC MUTATED APC WILD-TYPE
  RECTAL ADENOCARCINOMA                   95            11
  RECTAL MUCINOUS ADENOCARCINOMA           7             3
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2 RX
  APC MUTATED   77  2  7  3
  APC WILD-TYPE 11  0  2  1
D1V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          77            11
  R1           2             0
  R2           7             2
  RX           3             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"
D1V11, continuous

Clustering(2) Variable = CRIPAK MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED   10  1
  CRIPAK WILD-TYPE 85 20
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              105 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               1               20 
$`CRIPAK MUTATED`
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2693 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 
       26.43        46.92        37.97        33.17        31.00        13.97 
TCGA-DY-A1DD TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6465 
       57.24        20.55        19.96        20.91        49.51 

$`CRIPAK WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2691 
       25.97        15.95        36.03        55.76        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       13.55        34.49        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 
       19.99        28.04        36.03        14.04         1.02        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       26.04        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        12.62       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       32.61         3.48        18.28         9.96        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
           13.97             0.99 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           57.24           126.44 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              31               24 
[1] "14.0 - 57.2 (31.0)" "1.0 - 126.4 (24.0)"
[1] "hr=" "2.9"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CRIPAK MUTATED         1        0         3         0         0          2
  CRIPAK WILD-TYPE      26        7        26         2         4          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRIPAK MUTATED            3          1        0         1
  CRIPAK WILD-TYPE         13          9       13         4
D2V3, multiclass
            clus
vv           CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                 1               26
  STAGE II                0                7
  STAGE IIA               3               26
  STAGE IIB               0                2
  STAGE III               0                4
  STAGE IIIA              2                2
  STAGE IIIB              3               13
  STAGE IIIC              1                9
  STAGE IV                0               13
  STAGE IVA               1                4
[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
  CRIPAK MUTATED    1  2  8  0
  CRIPAK WILD-TYPE  7 23 72  9
D2V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              1                7
  T2              2               23
  T3              8               72
  T4              0                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
  CRIPAK MUTATED    4  6  1
  CRIPAK WILD-TYPE 63 26 20
D2V5, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  N0              4               63
  N1              6               26
  N2              1               20
[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"
D2V6, binary
                  cls
clus                0  1
  CRIPAK MUTATED    8  1
  CRIPAK WILD-TYPE 84 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      8    1
  CRIPAK WILD-TYPE   84   16
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0              8               84
  1              1               16
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                0  1
  CRIPAK MUTATED    7  4
  CRIPAK WILD-TYPE 48 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      7    4
  CRIPAK WILD-TYPE   48   63
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE              7               48
  MALE                4               63
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                0  1
  CRIPAK MUTATED    9  1
  CRIPAK WILD-TYPE 68 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      9    1
  CRIPAK WILD-TYPE   68   15
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO               9               68
  YES              1               15
[1] 2 2
[1] FALSE
D2V9, binary
                  cls
clus                0  1
  CRIPAK MUTATED    9  1
  CRIPAK WILD-TYPE 97  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      9    1
  CRIPAK WILD-TYPE   97    9
                                clus
vv                               CRIPAK MUTATED CRIPAK WILD-TYPE
  RECTAL ADENOCARCINOMA                       9               97
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  CRIPAK MUTATED    8  0  0  0
  CRIPAK WILD-TYPE 80  2  9  4
D2V10, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  R0              8               80
  R1              0                2
  R2              0                9
  RX              0                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   72 13
  TP53 WILD-TYPE 23  8
  TP53 MUTATED TP53 WILD-TYPE 
            85             31 
  TP53 MUTATED TP53 WILD-TYPE 
            13              8 
$`TP53 MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39        13.94        19.99        17.03        17.03        15.95 
TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       55.76        46.92        39.48        43.04        37.97        34.49 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       29.98        24.36        20.02        24.59        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
        7.07        46.03         2.01        50.04         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
       19.99         7.99        37.02        32.98         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.95        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A00Y 
       28.04        36.03        14.04         1.02         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       37.02         9.07         1.02         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
       38.04       117.11        38.56        17.49        43.20         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         3.48        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        42.35        28.57        32.19        36.49 
TCGA-F5-6813 
       19.66 

$`TP53 WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A00H TCGA-AG-A015 TCGA-G5-6641 TCGA-AF-2692 TCGA-AF-5654 
        8.02        25.97        36.03        26.43        13.55        16.83 
TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
       36.03        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       12.03         6.05         0.99         0.99        19.04         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-A002 TCGA-AG-A008 
       36.95        13.02        14.01        25.02        20.98        13.94 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6547 TCGA-AH-6644 TCGA-DC-6681 TCGA-DY-A1H8 
       49.97        38.96         2.50        27.55        25.97        32.61 
TCGA-F5-6465 
       49.51 

  TP53 MUTATED TP53 WILD-TYPE 
          0.99           0.99 
  TP53 MUTATED TP53 WILD-TYPE 
        126.44          49.97 
  TP53 MUTATED TP53 WILD-TYPE 
         24.59          20.98 
[1] "1.0 - 126.4 (24.6)" "1.0 - 50.0 (21.0)" 
[1] "hr=" "2.8"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TP53 MUTATED        17        6        22         2         2          2
  TP53 WILD-TYPE      10        1         7         0         2          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED           15          9        9         4
  TP53 WILD-TYPE          1          1        4         1
D3V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              17             10
  STAGE II              6              1
  STAGE IIA            22              7
  STAGE IIB             2              0
  STAGE III             2              2
  STAGE IIIA            2              2
  STAGE IIIB           15              1
  STAGE IIIC            9              1
  STAGE IV              9              4
  STAGE IVA             4              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
  TP53 MUTATED    3 17 62  9
  TP53 WILD-TYPE  5  8 18  0
D3V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            3              5
  T2           17              8
  T3           62             18
  T4            9              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"
                vv
clus             N0 N1 N2
  TP53 MUTATED   48 26 16
  TP53 WILD-TYPE 19  6  5
D3V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           48             19
  N1           26              6
  N2           16              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus              0  1
  TP53 MUTATED   69 12
  TP53 WILD-TYPE 23  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     69   12
  TP53 WILD-TYPE   23    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           69             23
  1           12              5
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus              0  1
  TP53 MUTATED   39 52
  TP53 WILD-TYPE 16 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     39   52
  TP53 WILD-TYPE   16   15
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           39             16
  MALE             52             15
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus              0  1
  TP53 MUTATED   57 11
  TP53 WILD-TYPE 20  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     57   11
  TP53 WILD-TYPE   20    5
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            57             20
  YES           11              5
[1] 2 2
[1] FALSE
D3V9, binary
                cls
clus              0  1
  TP53 MUTATED   84  5
  TP53 WILD-TYPE 22  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     84    5
  TP53 WILD-TYPE   22    5
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  RECTAL ADENOCARCINOMA                    84             22
  RECTAL MUCINOUS ADENOCARCINOMA            5              5
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   65  2  5  4
  TP53 WILD-TYPE 23  0  4  0
D3V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           65             23
  R1            2              0
  R2            5              4
  RX            4              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous

Clustering(4) Variable = NRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  NRAS MUTATED    9  1
  NRAS WILD-TYPE 86 20
  NRAS MUTATED NRAS WILD-TYPE 
            10            106 
  NRAS MUTATED NRAS WILD-TYPE 
             1             20 
$`NRAS MUTATED`
TCGA-AF-3913 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-3894 TCGA-DC-5337 
       10.39        43.04        24.36        13.02        14.01        26.04 
TCGA-DC-6160 TCGA-DC-6682 TCGA-EI-6510 TCGA-F5-6465 
       44.02        25.05        18.28        49.51 

$`NRAS WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 
       15.95        36.03        55.76        26.43        46.92        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 
       19.04        19.99         1.02        17.95        36.95        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        2.50        17.49        43.20        27.55         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       13.78        44.78        48.20        78.12         7.17        31.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       13.97        51.98        10.98        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6571 
        3.48        20.55        19.96        20.91         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  NRAS MUTATED NRAS WILD-TYPE 
         10.39           0.99 
  NRAS MUTATED NRAS WILD-TYPE 
         49.51         126.44 
  NRAS MUTATED NRAS WILD-TYPE 
        24.705         24.065 
[1] "10.4 - 49.5 (24.7)" "1.0 - 126.4 (24.1)"
[1] "hr=" "2"  
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  NRAS MUTATED         4        0         3         0         0          0
  NRAS WILD-TYPE      23        7        26         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED            2          0        1         0
  NRAS WILD-TYPE         14         10       12         5
D4V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               4             23
  STAGE II              0              7
  STAGE IIA             3             26
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            2             14
  STAGE IIIC            0             10
  STAGE IV              1             12
  STAGE IVA             0              5
[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    3  2  6  0
  NRAS WILD-TYPE  5 23 74  9
D4V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            3              5
  T2            2             23
  T3            6             74
  T4            0              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
  NRAS MUTATED    8  3  0
  NRAS WILD-TYPE 59 29 21
D4V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            8             59
  N1            3             29
  N2            0             21
[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"
D4V6, binary
                cls
clus              0  1
  NRAS MUTATED    8  1
  NRAS WILD-TYPE 84 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      8    1
  NRAS WILD-TYPE   84   16
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            8             84
  1            1             16
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus              0  1
  NRAS MUTATED    5  6
  NRAS WILD-TYPE 50 61
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    6
  NRAS WILD-TYPE   50   61
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            5             50
  MALE              6             61
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus              0  1
  NRAS MUTATED    8  2
  NRAS WILD-TYPE 69 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      8    2
  NRAS WILD-TYPE   69   14
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             8             69
  YES            2             14
[1] 2 2
[1] FALSE
D4V9, binary
                cls
clus              0  1
  NRAS MUTATED   11  0
  NRAS WILD-TYPE 95 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     11    0
  NRAS WILD-TYPE   95   10
                                clus
vv                               NRAS MUTATED NRAS WILD-TYPE
  RECTAL ADENOCARCINOMA                    11             95
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  NRAS MUTATED   10  0  0  0
  NRAS WILD-TYPE 78  2  9  4
D4V10, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           10             78
  R1            0              2
  R2            0              9
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous

Clustering(5) Variable = FMN2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  FMN2 MUTATED   10  4
  FMN2 WILD-TYPE 85 17
  FMN2 MUTATED FMN2 WILD-TYPE 
            14            102 
  FMN2 MUTATED FMN2 WILD-TYPE 
             4             17 
$`FMN2 MUTATED`
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-A026 TCGA-AH-6547 TCGA-CI-6619 
       32.98        19.04        19.99         1.94         2.50         6.05 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5869 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       44.78        78.12        31.00        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DG 
       41.36        51.48 

$`FMN2 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 
       19.99        28.04        36.03        14.04         1.02        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6621 
       38.56        17.49        43.20        27.55        33.17        13.78 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       48.20         7.17        26.04        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       44.02        25.97        25.05        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        3.48        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 

  FMN2 MUTATED FMN2 WILD-TYPE 
          1.94           0.99 
  FMN2 MUTATED FMN2 WILD-TYPE 
        126.44         117.11 
  FMN2 MUTATED FMN2 WILD-TYPE 
        28.025         24.065 
[1] "1.9 - 126.4 (28.0)" "1.0 - 117.1 (24.1)"
[1] "hr=" "1.1"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FMN2 MUTATED         2        2         4         1         0          0
  FMN2 WILD-TYPE      25        5        25         1         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMN2 MUTATED            1          1        1         1
  FMN2 WILD-TYPE         15          9       12         4
D5V3, multiclass
            clus
vv           FMN2 MUTATED FMN2 WILD-TYPE
  STAGE I               2             25
  STAGE II              2              5
  STAGE IIA             4             25
  STAGE IIB             1              1
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            1             15
  STAGE IIIC            1              9
  STAGE IV              1             12
  STAGE IVA             1              4
[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
  FMN2 MUTATED    0  2 10  2
  FMN2 WILD-TYPE  8 23 70  7
D5V4, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  T1            0              8
  T2            2             23
  T3           10             70
  T4            2              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  FMN2 MUTATED   10  3  1
  FMN2 WILD-TYPE 57 29 20
D5V5, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  N0           10             57
  N1            3             29
  N2            1             20
[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"
D5V6, binary
                cls
clus              0  1
  FMN2 MUTATED   10  2
  FMN2 WILD-TYPE 82 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     10    2
  FMN2 WILD-TYPE   82   15
   clus
vv  FMN2 MUTATED FMN2 WILD-TYPE
  0           10             82
  1            2             15
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus              0  1
  FMN2 MUTATED    8  6
  FMN2 WILD-TYPE 47 61
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED      8    6
  FMN2 WILD-TYPE   47   61
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  FEMALE            8             47
  MALE              6             61
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus              0  1
  FMN2 MUTATED    7  2
  FMN2 WILD-TYPE 70 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED      7    2
  FMN2 WILD-TYPE   70   14
     clus
vv    FMN2 MUTATED FMN2 WILD-TYPE
  NO             7             70
  YES            2             14
[1] 2 2
[1] FALSE
D5V9, binary
                cls
clus              0  1
  FMN2 MUTATED   12  1
  FMN2 WILD-TYPE 94  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     12    1
  FMN2 WILD-TYPE   94    9
                                clus
vv                               FMN2 MUTATED FMN2 WILD-TYPE
  RECTAL ADENOCARCINOMA                    12             94
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  FMN2 MUTATED    4  1  0  2
  FMN2 WILD-TYPE 84  1  9  2
D5V10, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  R0            4             84
  R1            1              1
  R2            0              9
  RX            2              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous

Clustering(6) Variable = SHROOM4 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  SHROOM4 MUTATED    5  2
  SHROOM4 WILD-TYPE 90 19
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               109 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2                19 
$`SHROOM4 MUTATED`
TCGA-AF-5654 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 
       16.83         7.17        31.00        13.97        44.02        20.55 
TCGA-F5-6813 
       19.66 

$`SHROOM4 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       48.20        78.12        26.04        51.98        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         3.48        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        42.35        28.57        32.19 
TCGA-F5-6812 
       36.49 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             7.17              0.99 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            44.02            126.44 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            19.66             24.59 
[1] "7.2 - 44.0 (19.7)"  "1.0 - 126.4 (24.6)"
[1] "hr=" "2.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SHROOM4 MUTATED         2        0         2         0         0          1
  SHROOM4 WILD-TYPE      25        7        27         2         4          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SHROOM4 MUTATED            1          1        0         0
  SHROOM4 WILD-TYPE         15          9       13         5
D6V3, multiclass
            clus
vv           SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE I                  2                25
  STAGE II                 0                 7
  STAGE IIA                2                27
  STAGE IIB                0                 2
  STAGE III                0                 4
  STAGE IIIA               1                 3
  STAGE IIIB               1                15
  STAGE IIIC               1                 9
  STAGE IV                 0                13
  STAGE IVA                0                 5
[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
  SHROOM4 MUTATED    0  3  3  1
  SHROOM4 WILD-TYPE  8 22 77  8
D6V4, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1               0                 8
  T2               3                22
  T3               3                77
  T4               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  SHROOM4 MUTATED    4  2  1
  SHROOM4 WILD-TYPE 63 30 20
D6V5, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  N0               4                63
  N1               2                30
  N2               1                20
[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"
D6V6, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    6  0
  SHROOM4 WILD-TYPE 86 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      6    0
  SHROOM4 WILD-TYPE   86   17
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               6                86
  1               0                17
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    5  2
  SHROOM4 WILD-TYPE 50 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      5    2
  SHROOM4 WILD-TYPE   50   65
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               5                50
  MALE                 2                65
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    7  0
  SHROOM4 WILD-TYPE 70 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      7    0
  SHROOM4 WILD-TYPE   70   16
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                7                70
  YES               0                16
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    7  0
  SHROOM4 WILD-TYPE 99 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      7    0
  SHROOM4 WILD-TYPE   99   10
                                clus
vv                               SHROOM4 MUTATED SHROOM4 WILD-TYPE
  RECTAL ADENOCARCINOMA                        7                99
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  SHROOM4 MUTATED    6  0  0  1
  SHROOM4 WILD-TYPE 82  2  9  3
D6V10, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0               6                82
  R1               0                 2
  R2               0                 9
  RX               1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous

Clustering(7) Variable = RPTN MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  RPTN MUTATED    3  2
  RPTN WILD-TYPE 92 19
  RPTN MUTATED RPTN WILD-TYPE 
             5            111 
  RPTN MUTATED RPTN WILD-TYPE 
             2             19 
$`RPTN MUTATED`
TCGA-AG-3732 TCGA-AH-6549 TCGA-DC-5869 TCGA-DY-A1DF TCGA-F5-6464 
       32.98        17.49        31.00        24.13         9.96 

$`RPTN WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       41.00        38.04       117.11        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        26.04        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  RPTN MUTATED RPTN WILD-TYPE 
          9.96           0.99 
  RPTN MUTATED RPTN WILD-TYPE 
         32.98         126.44 
  RPTN MUTATED RPTN WILD-TYPE 
         24.13          24.36 
[1] "10.0 - 33.0 (24.1)" "1.0 - 126.4 (24.4)"
[1] "hr=" "3.9"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RPTN MUTATED         1        0         0         0         0          0
  RPTN WILD-TYPE      26        7        29         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPTN MUTATED            1          2        0         0
  RPTN WILD-TYPE         15          8       13         5
D7V3, multiclass
            clus
vv           RPTN MUTATED RPTN WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             0             29
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            1             15
  STAGE IIIC            2              8
  STAGE IV              0             13
  STAGE IVA             0              5
[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
  RPTN MUTATED    0  1  3  1
  RPTN WILD-TYPE  8 24 77  8
D7V4, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T1            0              8
  T2            1             24
  T3            3             77
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  RPTN MUTATED    1  1  2
  RPTN WILD-TYPE 66 31 19
D7V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0            1             66
  N1            1             31
  N2            2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                cls
clus              0  1
  RPTN MUTATED    4  0
  RPTN WILD-TYPE 88 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      4    0
  RPTN WILD-TYPE   88   17
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            4             88
  1            0             17
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus              0  1
  RPTN MUTATED    4  1
  RPTN WILD-TYPE 51 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      4    1
  RPTN WILD-TYPE   51   66
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            4             51
  MALE              1             66
[1] 2 2
[1] FALSE
D7V8, binary
                cls
clus              0  1
  RPTN MUTATED    4  0
  RPTN WILD-TYPE 73 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      4    0
  RPTN WILD-TYPE   73   16
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO             4             73
  YES            0             16
[1] 2 2
[1] FALSE
D7V9, binary
                cls
clus               0   1
  RPTN MUTATED     5   0
  RPTN WILD-TYPE 101  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      5    0
  RPTN WILD-TYPE  101   10
                                clus
vv                               RPTN MUTATED RPTN WILD-TYPE
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  RPTN MUTATED    3  0  0  1
  RPTN WILD-TYPE 85  2  9  3
D7V10, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            3             85
  R1            0              2
  R2            0              9
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous

Clustering(8) Variable = ARID1A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    8  3
  ARID1A WILD-TYPE 87 18
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              105 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               18 
$`ARID1A MUTATED`
TCGA-AG-A00H TCGA-AF-2687 TCGA-AF-2693 TCGA-AG-3574 TCGA-AG-3878 TCGA-AG-3892 
       25.97        46.92        37.97        36.03         0.99        13.02 
TCGA-AG-A025 TCGA-CI-6620 TCGA-CI-6624 TCGA-DY-A1DF TCGA-DY-A1DG 
       49.97        33.17        48.20        24.13        51.48 

$`ARID1A WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2691 
       15.95        36.03        55.76        26.43        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       13.55        34.49        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       24.59        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       37.02         9.07         1.02         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 
       43.20        27.55         6.05        13.78        44.78        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.99 
  ARID1A MUTATED ARID1A WILD-TYPE 
           51.48           126.44 
  ARID1A MUTATED ARID1A WILD-TYPE 
           36.03            20.98 
[1] "1.0 - 51.5 (36.0)"  "1.0 - 126.4 (21.0)"
[1] "hr=" "1.1"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ARID1A MUTATED         5        1         1         0         0          0
  ARID1A WILD-TYPE      22        6        28         2         4          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID1A MUTATED            0          2        0         2
  ARID1A WILD-TYPE         16          8       13         3
D8V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 5               22
  STAGE II                1                6
  STAGE IIA               1               28
  STAGE IIB               0                2
  STAGE III               0                4
  STAGE IIIA              0                4
  STAGE IIIB              0               16
  STAGE IIIC              2                8
  STAGE IV                0               13
  STAGE IVA               2                3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ARID1A MUTATED    2  3  6  0
  ARID1A WILD-TYPE  6 22 74  9
D8V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2                6
  T2              3               22
  T3              6               74
  T4              0                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
  ARID1A MUTATED    7  2  2
  ARID1A WILD-TYPE 60 30 19
D8V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              7               60
  N1              2               30
  N2              2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    8  2
  ARID1A WILD-TYPE 84 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8    2
  ARID1A WILD-TYPE   84   15
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              8               84
  1              2               15
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    6  5
  ARID1A WILD-TYPE 49 62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    5
  ARID1A WILD-TYPE   49   62
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              6               49
  MALE                5               62
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                0  1
  ARID1A MUTATED    4  2
  ARID1A WILD-TYPE 73 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    2
  ARID1A WILD-TYPE   73   14
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               4               73
  YES              2               14
[1] 2 2
[1] FALSE
D8V9, binary
                  cls
clus                0  1
  ARID1A MUTATED   10  0
  ARID1A WILD-TYPE 96 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     10    0
  ARID1A WILD-TYPE   96   10
                                clus
vv                               ARID1A MUTATED ARID1A WILD-TYPE
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  ARID1A MUTATED    6  0  0  0
  ARID1A WILD-TYPE 82  2  9  4
D8V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              6               82
  R1              0                2
  R2              0                9
  RX              0                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous

Clustering(9) Variable = CDH1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  CDH1 MUTATED   10  2
  CDH1 WILD-TYPE 85 19
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            104 
  CDH1 MUTATED CDH1 WILD-TYPE 
             2             19 
$`CDH1 MUTATED`
TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-6136 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3892 
       55.76        46.92        24.36        37.02        32.98        13.02 
TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-5337 TCGA-DY-A1DG TCGA-EF-5830 TCGA-F5-6465 
       38.56        43.20        26.04        51.48         3.48        49.51 

$`CDH1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2691 
       25.97        15.95        36.03        26.43        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        7.99         0.99         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         2.50        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        24.13        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

  CDH1 MUTATED CDH1 WILD-TYPE 
          3.48           0.99 
  CDH1 MUTATED CDH1 WILD-TYPE 
         55.76         126.44 
  CDH1 MUTATED CDH1 WILD-TYPE 
        37.790         20.945 
[1] "3.5 - 55.8 (37.8)"  "1.0 - 126.4 (20.9)"
[1] "hr=" "1.9"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CDH1 MUTATED         3        0         1         1         0          0
  CDH1 WILD-TYPE      24        7        28         1         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH1 MUTATED            2          2        1         1
  CDH1 WILD-TYPE         14          8       12         4
D9V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I               3             24
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             1              1
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            2             14
  STAGE IIIC            2              8
  STAGE IV              1             12
  STAGE IVA             1              4
[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
  CDH1 MUTATED    2  1  8  1
  CDH1 WILD-TYPE  6 24 72  8
D9V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            2              6
  T2            1             24
  T3            8             72
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  CDH1 MUTATED    5  5  2
  CDH1 WILD-TYPE 62 27 19
D9V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            5             62
  N1            5             27
  N2            2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                cls
clus              0  1
  CDH1 MUTATED    7  3
  CDH1 WILD-TYPE 85 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      7    3
  CDH1 WILD-TYPE   85   14
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0            7             85
  1            3             14
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus              0  1
  CDH1 MUTATED    4  8
  CDH1 WILD-TYPE 51 59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      4    8
  CDH1 WILD-TYPE   51   59
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE            4             51
  MALE              8             59
[1] 2 2
[1] FALSE
D9V8, binary
                cls
clus              0  1
  CDH1 MUTATED    9  2
  CDH1 WILD-TYPE 68 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      9    2
  CDH1 WILD-TYPE   68   14
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO             9             68
  YES            2             14
[1] 2 2
[1] FALSE
D9V9, binary
                cls
clus              0  1
  CDH1 MUTATED   12  0
  CDH1 WILD-TYPE 94 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     12    0
  CDH1 WILD-TYPE   94   10
                                clus
vv                               CDH1 MUTATED CDH1 WILD-TYPE
  RECTAL ADENOCARCINOMA                    12             94
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  CDH1 MUTATED    7  1  1  0
  CDH1 WILD-TYPE 81  1  8  4
D9V10, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0            7             81
  R1            1              1
  R2            1              8
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous

Clustering(10) Variable = RBM10 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  RBM10 MUTATED    4  2
  RBM10 WILD-TYPE 91 19
  RBM10 MUTATED RBM10 WILD-TYPE 
              6             110 
  RBM10 MUTATED RBM10 WILD-TYPE 
              2              19 
$`RBM10 MUTATED`
TCGA-AF-2689 TCGA-AG-3583 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A002 TCGA-EI-6510 
       39.48        20.05        32.02        28.04        20.98        18.28 

$`RBM10 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        2.50        17.49        43.20        27.55         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       13.78        44.78        48.20        78.12         7.17        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

  RBM10 MUTATED RBM10 WILD-TYPE 
          18.28            0.99 
  RBM10 MUTATED RBM10 WILD-TYPE 
          39.48          126.44 
  RBM10 MUTATED RBM10 WILD-TYPE 
         24.510          24.245 
[1] "18.3 - 39.5 (24.5)" "1.0 - 126.4 (24.2)"
[1] "hr=" "2.4"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RBM10 MUTATED         1        0         1         0         0          0
  RBM10 WILD-TYPE      26        7        28         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM10 MUTATED            0          1        2         0
  RBM10 WILD-TYPE         16          9       11         5
D10V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                1              26
  STAGE II               0               7
  STAGE IIA              1              28
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             1               9
  STAGE IV               2              11
  STAGE IVA              0               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  RBM10 MUTATED    0  2  4  0
  RBM10 WILD-TYPE  8 23 76  9
D10V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             0               8
  T2             2              23
  T3             4              76
  T4             0               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
  RBM10 MUTATED    3  0  3
  RBM10 WILD-TYPE 64 32 18
D10V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0             3              64
  N1             0              32
  N2             3              18
[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"
D10V6, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  2
  RBM10 WILD-TYPE 89 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    2
  RBM10 WILD-TYPE   89   15
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             3              89
  1             2              15
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  3
  RBM10 WILD-TYPE 52 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    3
  RBM10 WILD-TYPE   52   64
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             3              52
  MALE               3              64
[1] 2 2
[1] FALSE
D10V8, binary
                 cls
clus               0  1
  RBM10 MUTATED    6  0
  RBM10 WILD-TYPE 71 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      6    0
  RBM10 WILD-TYPE   71   16
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              6              71
  YES             0              16
[1] 2 2
[1] FALSE
D10V9, binary
                 cls
clus                0   1
  RBM10 MUTATED     5   1
  RBM10 WILD-TYPE 101   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      5    1
  RBM10 WILD-TYPE  101    9
                                clus
vv                               RBM10 MUTATED RBM10 WILD-TYPE
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  RBM10 MUTATED    5  0  1  0
  RBM10 WILD-TYPE 83  2  8  4
D10V10, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             5              83
  R1             0               2
  R2             1               8
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous

Clustering(11) Variable = HAUS6 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  HAUS6 MUTATED    5  0
  HAUS6 WILD-TYPE 90 21
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              5             111 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              0              21 
$`HAUS6 MUTATED`
TCGA-AG-3742 TCGA-AG-3892 TCGA-CI-6621 TCGA-EI-6506 TCGA-F5-6465 
        0.99        13.02        13.78        20.55        49.51 

$`HAUS6 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
       27.55         6.05        33.17        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
           0.99            0.99 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          49.51          126.44 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          13.78           24.59 
[1] "1.0 - 49.5 (13.8)"  "1.0 - 126.4 (24.6)"
[1] "hr="     "2.6e+07"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  HAUS6 MUTATED         2        0         2         0         0          0
  HAUS6 WILD-TYPE      25        7        27         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS6 MUTATED            1          0        0         0
  HAUS6 WILD-TYPE         15         10       13         5
D11V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                2              25
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             1              15
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[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
  HAUS6 MUTATED    2  0  3  0
  HAUS6 WILD-TYPE  6 25 77  9
D11V4, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             2               6
  T2             0              25
  T3             3              77
  T4             0               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
  HAUS6 MUTATED    4  1  0
  HAUS6 WILD-TYPE 63 31 21
D11V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             4              63
  N1             1              31
  N2             0              21
[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"
D11V6, binary
                 cls
clus               0  1
  HAUS6 MUTATED    4  0
  HAUS6 WILD-TYPE 88 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      4    0
  HAUS6 WILD-TYPE   88   17
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0             4              88
  1             0              17
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus               0  1
  HAUS6 MUTATED    4  1
  HAUS6 WILD-TYPE 51 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      4    1
  HAUS6 WILD-TYPE   51   66
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE             4              51
  MALE               1              66
[1] 2 2
[1] FALSE
D11V8, binary
                 cls
clus               0  1
  HAUS6 MUTATED    3  0
  HAUS6 WILD-TYPE 74 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      3    0
  HAUS6 WILD-TYPE   74   16
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO              3              74
  YES             0              16
[1] 2 2
[1] FALSE
D11V9, binary
                 cls
clus                0   1
  HAUS6 MUTATED     5   0
  HAUS6 WILD-TYPE 101  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      5    0
  HAUS6 WILD-TYPE  101   10
                                clus
vv                               HAUS6 MUTATED HAUS6 WILD-TYPE
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  HAUS6 MUTATED    4  0  0  0
  HAUS6 WILD-TYPE 84  2  9  4
D11V10, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0             4              84
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous

Clustering(12) Variable = CTNNB1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED   15  4
  CTNNB1 WILD-TYPE 80 17
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19               97 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4               17 
$`CTNNB1 MUTATED`
TCGA-AF-2693 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 
       37.97        20.02        12.00        32.98        19.04        13.02 
TCGA-AG-A020 TCGA-AH-6547 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6682 TCGA-DY-A0XA 
        1.02         2.50        78.12        26.04        25.05       126.44 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       24.13        51.48        18.28        49.51        42.35        32.19 
TCGA-F5-6813 
       19.66 

$`CTNNB1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.36        24.59        36.03        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        37.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       37.02         9.07        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11        38.56        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
       25.97        25.05        12.62        41.36        57.24        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6702 
        3.48        20.55        19.96        20.91         9.96        28.57 
TCGA-F5-6812 
       36.49 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            1.02             0.99 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          126.44           117.11 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           25.05            24.00 
[1] "1.0 - 126.4 (25.1)" "1.0 - 117.1 (24.0)"
[1] "hr=" "1.1"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CTNNB1 MUTATED         4        1         6         0         1          1
  CTNNB1 WILD-TYPE      23        6        23         2         3          3
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTNNB1 MUTATED            0          3        0         1
  CTNNB1 WILD-TYPE         16          7       13         4
D12V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 4               23
  STAGE II                1                6
  STAGE IIA               6               23
  STAGE IIB               0                2
  STAGE III               1                3
  STAGE IIIA              1                3
  STAGE IIIB              0               16
  STAGE IIIC              3                7
  STAGE IV                0               13
  STAGE IVA               1                4
[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
  CTNNB1 MUTATED    2  4 12  1
  CTNNB1 WILD-TYPE  6 21 68  8
D12V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              2                6
  T2              4               21
  T3             12               68
  T4              1                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  CTNNB1 MUTATED   13  3  3
  CTNNB1 WILD-TYPE 54 29 18
D12V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             13               54
  N1              3               29
  N2              3               18
[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"
D12V6, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   14  1
  CTNNB1 WILD-TYPE 78 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     14    1
  CTNNB1 WILD-TYPE   78   16
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             14               78
  1              1               16
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   12  7
  CTNNB1 WILD-TYPE 43 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     12    7
  CTNNB1 WILD-TYPE   43   60
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             12               43
  MALE                7               60
[1] 2 2
[1] FALSE
D12V8, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   15  0
  CTNNB1 WILD-TYPE 62 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     15    0
  CTNNB1 WILD-TYPE   62   16
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              15               62
  YES              0               16
[1] 2 2
[1] FALSE
D12V9, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   16  1
  CTNNB1 WILD-TYPE 90  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     16    1
  CTNNB1 WILD-TYPE   90    9
                                clus
vv                               CTNNB1 MUTATED CTNNB1 WILD-TYPE
  RECTAL ADENOCARCINOMA                      16               90
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  CTNNB1 MUTATED   11  0  0  1
  CTNNB1 WILD-TYPE 77  2  9  3
D12V10, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             11               77
  R1              0                2
  R2              0                9
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous

Clustering(13) Variable = GABRP MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  GABRP MUTATED    4  0
  GABRP WILD-TYPE 91 21
  GABRP MUTATED GABRP WILD-TYPE 
              4             112 
  GABRP MUTATED GABRP WILD-TYPE 
              0              21 
$`GABRP MUTATED`
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A02N TCGA-EF-5830 
       32.98        13.02        61.97         3.48 

$`GABRP WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  GABRP MUTATED GABRP WILD-TYPE 
           3.48            0.99 
  GABRP MUTATED GABRP WILD-TYPE 
          61.97          126.44 
  GABRP MUTATED GABRP WILD-TYPE 
         23.000          24.245 
[1] "3.5 - 62.0 (23.0)"  "1.0 - 126.4 (24.2)"
[1] "hr="     "2.8e+07"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  GABRP MUTATED         2        1         0         1         0          0
  GABRP WILD-TYPE      25        6        29         1         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABRP MUTATED            0          0        0         0
  GABRP WILD-TYPE         16         10       13         5
D13V3, multiclass
            clus
vv           GABRP MUTATED GABRP WILD-TYPE
  STAGE I                2              25
  STAGE II               1               6
  STAGE IIA              0              29
  STAGE IIB              1               1
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[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
  GABRP MUTATED    1  1  1  1
  GABRP WILD-TYPE  7 24 79  8
D13V4, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  T1             1               7
  T2             1              24
  T3             1              79
  T4             1               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  GABRP MUTATED    4  0  0
  GABRP WILD-TYPE 63 32 21
D13V5, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  N0             4              63
  N1             0              32
  N2             0              21
[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"
D13V6, binary
                 cls
clus               0  1
  GABRP MUTATED    4  0
  GABRP WILD-TYPE 88 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      4    0
  GABRP WILD-TYPE   88   17
   clus
vv  GABRP MUTATED GABRP WILD-TYPE
  0             4              88
  1             0              17
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus               0  1
  GABRP MUTATED    2  2
  GABRP WILD-TYPE 53 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      2    2
  GABRP WILD-TYPE   53   65
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  FEMALE             2              53
  MALE               2              65
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus               0  1
  GABRP MUTATED    3  0
  GABRP WILD-TYPE 74 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      3    0
  GABRP WILD-TYPE   74   16
     clus
vv    GABRP MUTATED GABRP WILD-TYPE
  NO              3              74
  YES             0              16
[1] 2 2
[1] FALSE
D13V9, binary
                 cls
clus                0   1
  GABRP MUTATED     4   0
  GABRP WILD-TYPE 102  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      4    0
  GABRP WILD-TYPE  102   10
                                clus
vv                               GABRP MUTATED GABRP WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  GABRP MUTATED    4  0  0  0
  GABRP WILD-TYPE 84  2  9  4
D13V10, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  R0             4              84
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous

Clustering(14) Variable = PON3 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  PON3 MUTATED    3  1
  PON3 WILD-TYPE 92 20
  PON3 MUTATED PON3 WILD-TYPE 
             4            112 
  PON3 MUTATED PON3 WILD-TYPE 
             1             20 
$`PON3 MUTATED`
TCGA-AF-2693 TCGA-CI-6620 TCGA-CL-5918 TCGA-DY-A1DG 
       37.97        33.17         7.17        51.48 

$`PON3 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       43.20        27.55         6.05        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  PON3 MUTATED PON3 WILD-TYPE 
          7.17           0.99 
  PON3 MUTATED PON3 WILD-TYPE 
         51.48         126.44 
  PON3 MUTATED PON3 WILD-TYPE 
        35.570         24.065 
[1] "7.2 - 51.5 (35.6)"  "1.0 - 126.4 (24.1)"
[1] "hr=" "1"  
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PON3 MUTATED         1        0         1         0         0          0
  PON3 WILD-TYPE      26        7        28         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PON3 MUTATED            0          0        0         2
  PON3 WILD-TYPE         16         10       13         3
D14V3, multiclass
            clus
vv           PON3 MUTATED PON3 WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            0             16
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             2              3
[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
  PON3 MUTATED    0  1  3  0
  PON3 WILD-TYPE  8 24 77  9
D14V4, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  T1            0              8
  T2            1             24
  T3            3             77
  T4            0              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
  PON3 MUTATED    2  2  0
  PON3 WILD-TYPE 65 30 21
D14V5, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  N0            2             65
  N1            2             30
  N2            0             21
[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"
D14V6, binary
                cls
clus              0  1
  PON3 MUTATED    0  2
  PON3 WILD-TYPE 92 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      0    2
  PON3 WILD-TYPE   92   15
   clus
vv  PON3 MUTATED PON3 WILD-TYPE
  0            0             92
  1            2             15
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus              0  1
  PON3 MUTATED    2  2
  PON3 WILD-TYPE 53 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      2    2
  PON3 WILD-TYPE   53   65
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  FEMALE            2             53
  MALE              2             65
[1] 2 2
[1] FALSE
D14V8, binary
                cls
clus              0  1
  PON3 MUTATED    3  0
  PON3 WILD-TYPE 74 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      3    0
  PON3 WILD-TYPE   74   16
     clus
vv    PON3 MUTATED PON3 WILD-TYPE
  NO             3             74
  YES            0             16
[1] 2 2
[1] FALSE
D14V9, binary
                cls
clus               0   1
  PON3 MUTATED     3   0
  PON3 WILD-TYPE 103  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      3    0
  PON3 WILD-TYPE  103   10
                                clus
vv                               PON3 MUTATED PON3 WILD-TYPE
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  PON3 MUTATED    0  0  0  1
  PON3 WILD-TYPE 88  2  9  3
D14V10, multiclass
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             1            102 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2687 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3581     TCGA-AG-3582 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3726     TCGA-AG-3727 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A016     TCGA-AG-A01L 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6549     TCGA-AH-6643 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-CL-5917     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" 
D14V11, continuous
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             2            112 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2687 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3892 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4015 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00Y 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A036     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6643 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-CI-6622     TCGA-DC-5337 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 

Clustering(15) Variable = RLIM MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  RLIM MUTATED    3  1
  RLIM WILD-TYPE 92 20
  RLIM MUTATED RLIM WILD-TYPE 
             4            112 
  RLIM MUTATED RLIM WILD-TYPE 
             1             20 
$`RLIM MUTATED`
TCGA-AF-2687 TCGA-AG-A002 TCGA-DY-A0XA TCGA-DY-A1DG 
       46.92        20.98       126.44        51.48 

$`RLIM WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 
       25.97        15.95        36.03        55.76        26.43        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        1.02        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  RLIM MUTATED RLIM WILD-TYPE 
         20.98           0.99 
  RLIM MUTATED RLIM WILD-TYPE 
        126.44         117.11 
  RLIM MUTATED RLIM WILD-TYPE 
        49.200         24.065 
[1] "21.0 - 126.4 (49.2)" "1.0 - 117.1 (24.1)" 
[1] "hr=" "2"  
D15V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RLIM MUTATED         1        0         1         0         0          0
  RLIM WILD-TYPE      26        7        28         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RLIM MUTATED            0          1        0         1
  RLIM WILD-TYPE         16          9       13         4
D15V3, multiclass
            clus
vv           RLIM MUTATED RLIM WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            0             16
  STAGE IIIC            1              9
  STAGE IV              0             13
  STAGE IVA             1              4
[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
  RLIM MUTATED    0  1  3  0
  RLIM WILD-TYPE  8 24 77  9
D15V4, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            0              8
  T2            1             24
  T3            3             77
  T4            0              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
  RLIM MUTATED    2  1  1
  RLIM WILD-TYPE 65 31 20
D15V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0            2             65
  N1            1             31
  N2            1             20
[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"
D15V6, binary
                cls
clus              0  1
  RLIM MUTATED    3  1
  RLIM WILD-TYPE 89 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      3    1
  RLIM WILD-TYPE   89   16
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0            3             89
  1            1             16
[1] 2 2
[1] FALSE
D15V7, binary
                cls
clus              0  1
  RLIM MUTATED    1  3
  RLIM WILD-TYPE 54 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      1    3
  RLIM WILD-TYPE   54   64
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  FEMALE            1             54
  MALE              3             64
[1] 2 2
[1] FALSE
D15V8, binary
                cls
clus              0  1
  RLIM MUTATED    1  1
  RLIM WILD-TYPE 76 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      1    1
  RLIM WILD-TYPE   76   15
     clus
vv    RLIM MUTATED RLIM WILD-TYPE
  NO             1             76
  YES            1             15
[1] 2 2
[1] FALSE
D15V9, binary
                cls
clus               0   1
  RLIM MUTATED     4   0
  RLIM WILD-TYPE 102  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      4    0
  RLIM WILD-TYPE  102   10
                                clus
vv                               RLIM MUTATED RLIM WILD-TYPE
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  RLIM MUTATED    2  0  0  0
  RLIM WILD-TYPE 86  2  9  4
D15V10, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             2            101 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2689 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400     TCGA-AF-4110 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3882 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3892 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4015 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00Y     TCGA-AG-A011 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-F5-6813 
"RLIM WILD-TYPE" 
D15V11, continuous

Clustering(16) Variable = SMAD2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2              0  1
  SMAD2 MUTATED    5  0
  SMAD2 WILD-TYPE 90 21
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              5             111 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              0              21 
$`SMAD2 MUTATED`
TCGA-AG-3890 TCGA-G5-6235 TCGA-AG-3608 TCGA-AG-A002 TCGA-F5-6465 
       17.03        55.76        15.95        20.98        49.51 

$`SMAD2 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       15.95        36.03        26.43        46.92        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        34.49        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        24.59        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 
       19.99        28.04        36.03        14.04         1.02        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         9.07         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         2.50        17.49        43.20        27.55         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
          15.95            0.99 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          55.76          126.44 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          20.98           24.36 
[1] "15.9 - 55.8 (21.0)" "1.0 - 126.4 (24.4)"
[1] "hr="     "7.4e+07"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD2 MUTATED         2        1         2         0         0          0
  SMAD2 WILD-TYPE      25        6        27         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED            1          0        0         0
  SMAD2 WILD-TYPE         15         10       13         5
D16V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                2              25
  STAGE II               1               6
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             1              15
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[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  2  4  0
  SMAD2 WILD-TYPE  8 23 76  9
D16V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               8
  T2             2              23
  T3             4              76
  T4             0               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
  SMAD2 MUTATED    5  1  0
  SMAD2 WILD-TYPE 62 31 21
D16V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             5              62
  N1             1              31
  N2             0              21
[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"
D16V6, binary
                 cls
clus               0  1
  SMAD2 MUTATED    5  0
  SMAD2 WILD-TYPE 87 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      5    0
  SMAD2 WILD-TYPE   87   17
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0             5              87
  1             0              17
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus               0  1
  SMAD2 MUTATED    3  3
  SMAD2 WILD-TYPE 52 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      3    3
  SMAD2 WILD-TYPE   52   64
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             3              52
  MALE               3              64
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus               0  1
  SMAD2 MUTATED    5  0
  SMAD2 WILD-TYPE 72 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      5    0
  SMAD2 WILD-TYPE   72   16
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO              5              72
  YES             0              16
[1] 2 2
[1] FALSE
D16V9, binary
                 cls
clus                0   1
  SMAD2 MUTATED     6   0
  SMAD2 WILD-TYPE 100  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      6    0
  SMAD2 WILD-TYPE  100   10
                                clus
vv                               SMAD2 MUTATED SMAD2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  SMAD2 MUTATED    5  1  0  0
  SMAD2 WILD-TYPE 83  1  9  4
D16V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             5              83
  R1             1               1
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous

Clustering(17) Variable = TCF7L2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2               0  1
  TCF7L2 MUTATED   10  2
  TCF7L2 WILD-TYPE 85 19
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              12              104 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               2               19 
$`TCF7L2 MUTATED`
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3726 TCGA-AG-3882 
       13.55        29.98        20.02        36.03         7.99        19.99 
TCGA-AG-3898 TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-DC-6683 TCGA-DY-A1DG 
       48.03        38.04        38.56         6.05        25.05        51.48 

$`TCF7L2 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6136 
       39.48        43.04        37.97        34.49        16.83        24.36 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       24.59        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 
       12.03         6.05         0.99        15.95        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       41.00       117.11         2.50        17.49        43.20        27.55 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         3.48        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            6.05             0.99 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           51.48           126.44 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
          27.515           24.065 
[1] "6.0 - 51.5 (27.5)"  "1.0 - 126.4 (24.1)"
[1] "hr=" "1.2"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TCF7L2 MUTATED         2        0         2         0         0          1
  TCF7L2 WILD-TYPE      25        7        27         2         4          3
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7L2 MUTATED            2          0        2         2
  TCF7L2 WILD-TYPE         14         10       11         3
D17V3, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 2               25
  STAGE II                0                7
  STAGE IIA               2               27
  STAGE IIB               0                2
  STAGE III               0                4
  STAGE IIIA              1                3
  STAGE IIIB              2               14
  STAGE IIIC              0               10
  STAGE IV                2               11
  STAGE IVA               2                3
[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  8  1
  TCF7L2 WILD-TYPE  8 22 72  8
D17V4, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                8
  T2              3               22
  T3              8               72
  T4              1                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  TCF7L2 MUTATED    4  7  1
  TCF7L2 WILD-TYPE 63 25 20
D17V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0              4               63
  N1              7               25
  N2              1               20
[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"
D17V6, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    7  4
  TCF7L2 WILD-TYPE 85 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      7    4
  TCF7L2 WILD-TYPE   85   13
   clus
vv  TCF7L2 MUTATED TCF7L2 WILD-TYPE
  0              7               85
  1              4               13
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    3  9
  TCF7L2 WILD-TYPE 52 58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      3    9
  TCF7L2 WILD-TYPE   52   58
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE              3               52
  MALE                9               58
[1] 2 2
[1] FALSE
D17V8, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    9  1
  TCF7L2 WILD-TYPE 68 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      9    1
  TCF7L2 WILD-TYPE   68   15
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  NO               9               68
  YES              1               15
[1] 2 2
[1] FALSE
D17V9, binary
                  cls
clus                0  1
  TCF7L2 MUTATED   10  0
  TCF7L2 WILD-TYPE 96 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     10    0
  TCF7L2 WILD-TYPE   96   10
                                clus
vv                               TCF7L2 MUTATED TCF7L2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  TCF7L2 MUTATED    8  0  1  0
  TCF7L2 WILD-TYPE 80  2  8  4
D17V10, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0              8               80
  R1              0                2
  R2              1                8
  RX              0                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous

Clustering(18) Variable = OXSM MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  OXSM MUTATED    4  0
  OXSM WILD-TYPE 91 21
  OXSM MUTATED OXSM WILD-TYPE 
             4            112 
  OXSM MUTATED OXSM WILD-TYPE 
             0             21 
$`OXSM MUTATED`
TCGA-AG-3892 TCGA-CL-5918 TCGA-DC-6682 TCGA-DT-5265 
       13.02         7.17        25.05        12.62 

$`OXSM WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       48.20        78.12        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.97        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  OXSM MUTATED OXSM WILD-TYPE 
          7.17           0.99 
  OXSM MUTATED OXSM WILD-TYPE 
         25.05         126.44 
  OXSM MUTATED OXSM WILD-TYPE 
        12.820         24.475 
[1] "7.2 - 25.1 (12.8)"  "1.0 - 126.4 (24.5)"
[1] "hr="     "9300000"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  OXSM MUTATED         1        1         2         0         0          0
  OXSM WILD-TYPE      26        6        27         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OXSM MUTATED            0          0        0         0
  OXSM WILD-TYPE         16         10       13         5
D18V3, multiclass
            clus
vv           OXSM MUTATED OXSM WILD-TYPE
  STAGE I               1             26
  STAGE II              1              6
  STAGE IIA             2             27
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            0             16
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             0              5
[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
  OXSM MUTATED    1  0  3  0
  OXSM WILD-TYPE  7 25 77  9
D18V4, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  T1            1              7
  T2            0             25
  T3            3             77
  T4            0              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
  OXSM MUTATED    4  0  0
  OXSM WILD-TYPE 63 32 21
D18V5, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  N0            4             63
  N1            0             32
  N2            0             21
[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"
D18V6, binary
                cls
clus              0  1
  OXSM MUTATED    3  0
  OXSM WILD-TYPE 89 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      3    0
  OXSM WILD-TYPE   89   17
   clus
vv  OXSM MUTATED OXSM WILD-TYPE
  0            3             89
  1            0             17
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus              0  1
  OXSM MUTATED    2  2
  OXSM WILD-TYPE 53 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      2    2
  OXSM WILD-TYPE   53   65
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  FEMALE            2             53
  MALE              2             65
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus              0  1
  OXSM MUTATED    3  1
  OXSM WILD-TYPE 74 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      3    1
  OXSM WILD-TYPE   74   15
     clus
vv    OXSM MUTATED OXSM WILD-TYPE
  NO             3             74
  YES            1             15
[1] 2 2
[1] FALSE
D18V9, binary
                cls
clus               0   1
  OXSM MUTATED     3   1
  OXSM WILD-TYPE 103   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      3    1
  OXSM WILD-TYPE  103    9
                                clus
vv                               OXSM MUTATED OXSM WILD-TYPE
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  OXSM MUTATED    2  0  0  2
  OXSM WILD-TYPE 86  2  9  2
D18V10, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  R0            2             86
  R1            0              2
  R2            0              9
  RX            2              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             2            112 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2687 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-2693 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574     TCGA-AG-3575 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4015 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00Y 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A036     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6643 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6621     TCGA-CI-6622     TCGA-DC-5337 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6683     TCGA-DY-A0XA 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 

Clustering(19) Variable = PCBP1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  PCBP1 MUTATED    5  0
  PCBP1 WILD-TYPE 90 21
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              5             111 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              21 
$`PCBP1 MUTATED`
TCGA-AG-3894 TCGA-AG-A002 TCGA-AH-6544 TCGA-CI-6622 TCGA-F5-6465 
       14.01        20.98        38.56        44.78        49.51 

$`PCBP1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        35.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        1.02        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17        13.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
          14.01            0.99 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          49.51          126.44 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          38.56           24.13 
[1] "14.0 - 49.5 (38.6)" "1.0 - 126.4 (24.1)"
[1] "hr="     "7.4e+07"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCBP1 MUTATED         1        0         2         1         0          0
  PCBP1 WILD-TYPE      26        7        27         1         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED            0          0        0         0
  PCBP1 WILD-TYPE         16         10       13         5
D19V3, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                1              26
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              1               1
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  PCBP1 MUTATED    0  1  3  1
  PCBP1 WILD-TYPE  8 24 77  8
D19V4, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               8
  T2             1              24
  T3             3              77
  T4             1               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  PCBP1 MUTATED    4  1  0
  PCBP1 WILD-TYPE 63 31 21
D19V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0             4              63
  N1             1              31
  N2             0              21
[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"
D19V6, binary
                 cls
clus               0  1
  PCBP1 MUTATED    4  1
  PCBP1 WILD-TYPE 88 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      4    1
  PCBP1 WILD-TYPE   88   16
   clus
vv  PCBP1 MUTATED PCBP1 WILD-TYPE
  0             4              88
  1             1              16
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus               0  1
  PCBP1 MUTATED    1  4
  PCBP1 WILD-TYPE 54 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      1    4
  PCBP1 WILD-TYPE   54   63
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             1              54
  MALE               4              63
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus               0  1
  PCBP1 MUTATED    3  2
  PCBP1 WILD-TYPE 74 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      3    2
  PCBP1 WILD-TYPE   74   14
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  NO              3              74
  YES             2              14
[1] 2 2
[1] FALSE
D19V9, binary
                 cls
clus                0   1
  PCBP1 MUTATED     5   0
  PCBP1 WILD-TYPE 101  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      5    0
  PCBP1 WILD-TYPE  101   10
                                clus
vv                               PCBP1 MUTATED PCBP1 WILD-TYPE
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  PCBP1 MUTATED    3  0  0  0
  PCBP1 WILD-TYPE 85  2  9  4
D19V10, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             3              85
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous

Clustering(20) Variable = KRAS MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   54  7
  KRAS WILD-TYPE 41 14
  KRAS MUTATED KRAS WILD-TYPE 
            61             55 
  KRAS MUTATED KRAS WILD-TYPE 
             7             14 
$`KRAS MUTATED`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
        8.02        13.94        17.03        25.97        15.95        36.03 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-5654 
       55.76        39.48        43.04        13.55        29.98        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       20.02        24.59        12.00         7.07        20.05         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        2.01        12.03         0.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 
        0.99         0.99        17.95        36.95        13.02         1.02 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 
       25.02        32.02        19.99        28.04        14.04        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        6.02        23.01         1.02        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 
       38.04        38.56        17.49        27.55        33.17        44.78 
TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1H8 
       78.12        13.97        44.02        25.05        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6571 TCGA-F5-6702 
        3.48        20.55        19.96        18.28        42.35        28.57 
TCGA-F5-6812 
       36.49 

$`KRAS WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-3890 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2693 
       10.39        19.99        17.03        26.43        46.92        37.97 
TCGA-AF-3400 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       34.49        24.36        36.03        32.02        36.03        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       46.03        34.03        50.04         6.05        15.95        19.99 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3894 
       32.98        19.04        19.99         1.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 
       48.03        36.03         1.02        20.98        37.02         9.07 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6619 
        1.94        38.96       117.11         2.50        43.20         6.05 
TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 
       13.78        48.20         7.17        26.04        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 
       57.24        51.48        20.91         9.96        49.51        32.19 
TCGA-F5-6813 
       19.66 

  KRAS MUTATED KRAS WILD-TYPE 
          0.99           1.02 
  KRAS MUTATED KRAS WILD-TYPE 
         78.12         126.44 
  KRAS MUTATED KRAS WILD-TYPE 
         20.05          26.04 
[1] "1.0 - 78.1 (20.1)"  "1.0 - 126.4 (26.0)"
[1] "hr=" "1.7"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KRAS MUTATED        16        3        12         2         3          3
  KRAS WILD-TYPE      11        4        17         0         1          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED            7          4        6         3
  KRAS WILD-TYPE          9          6        7         2
D20V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              16             11
  STAGE II              3              4
  STAGE IIA            12             17
  STAGE IIB             2              0
  STAGE III             3              1
  STAGE IIIA            3              1
  STAGE IIIB            7              9
  STAGE IIIC            4              6
  STAGE IV              6              7
  STAGE IVA             3              2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  KRAS MUTATED    6 14 39  4
  KRAS WILD-TYPE  2 11 41  5
D20V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            6              2
  T2           14             11
  T3           39             41
  T4            4              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
  KRAS MUTATED   34 17 10
  KRAS WILD-TYPE 33 15 11
D20V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           34             33
  N1           17             15
  N2           10             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"
D20V6, binary
                cls
clus              0  1
  KRAS MUTATED   48  8
  KRAS WILD-TYPE 44  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     48    8
  KRAS WILD-TYPE   44    9
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           48             44
  1            8              9
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus              0  1
  KRAS MUTATED   30 33
  KRAS WILD-TYPE 25 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     30   33
  KRAS WILD-TYPE   25   34
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           30             25
  MALE             33             34
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus              0  1
  KRAS MUTATED   41  7
  KRAS WILD-TYPE 36  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     41    7
  KRAS WILD-TYPE   36    9
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            41             36
  YES            7              9
[1] 2 2
[1] FALSE
D20V9, binary
                cls
clus              0  1
  KRAS MUTATED   53  6
  KRAS WILD-TYPE 53  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     53    6
  KRAS WILD-TYPE   53    4
                                clus
vv                               KRAS MUTATED KRAS WILD-TYPE
  RECTAL ADENOCARCINOMA                    53             53
  RECTAL MUCINOUS ADENOCARCINOMA            6              4
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   50  1  3  2
  KRAS WILD-TYPE 38  1  6  2
D20V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           50             38
  R1            1              1
  R2            3              6
  RX            2              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous

Clustering(21) Variable = FLT1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2             0  1
  FLT1 MUTATED    6  2
  FLT1 WILD-TYPE 89 19
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            108 
  FLT1 MUTATED FLT1 WILD-TYPE 
             2             19 
$`FLT1 MUTATED`
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3878 TCGA-AG-A002 TCGA-DY-A0XA 
       29.98        16.83        24.36         0.99        20.98       126.44 
TCGA-DY-A1DD TCGA-EI-6507 
       57.24        19.96 

$`FLT1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-6655 
       39.48        43.04        13.55        37.97        34.49        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        2.50        17.49        43.20        27.55         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       13.78        44.78        48.20        78.12         7.17        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        25.05        12.62        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         3.48        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 

  FLT1 MUTATED FLT1 WILD-TYPE 
          0.99           0.99 
  FLT1 MUTATED FLT1 WILD-TYPE 
        126.44         117.11 
  FLT1 MUTATED FLT1 WILD-TYPE 
         22.67          24.36 
[1] "1.0 - 126.4 (22.7)" "1.0 - 117.1 (24.4)"
[1] "hr=" "1"  
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FLT1 MUTATED         3        0         2         0         0          0
  FLT1 WILD-TYPE      24        7        27         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLT1 MUTATED            2          0        0         1
  FLT1 WILD-TYPE         14         10       13         4
D21V3, multiclass
            clus
vv           FLT1 MUTATED FLT1 WILD-TYPE
  STAGE I               3             24
  STAGE II              0              7
  STAGE IIA             2             27
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            2             14
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             1              4
[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
  FLT1 MUTATED    0  3  4  1
  FLT1 WILD-TYPE  8 22 76  8
D21V4, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  T1            0              8
  T2            3             22
  T3            4             76
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  FLT1 MUTATED    5  2  1
  FLT1 WILD-TYPE 62 30 20
D21V5, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  N0            5             62
  N1            2             30
  N2            1             20
[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"
D21V6, binary
                cls
clus              0  1
  FLT1 MUTATED    6  0
  FLT1 WILD-TYPE 86 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED      6    0
  FLT1 WILD-TYPE   86   17
   clus
vv  FLT1 MUTATED FLT1 WILD-TYPE
  0            6             86
  1            0             17
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus              0  1
  FLT1 MUTATED    4  4
  FLT1 WILD-TYPE 51 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED      4    4
  FLT1 WILD-TYPE   51   63
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  FEMALE            4             51
  MALE              4             63
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus              0  1
  FLT1 MUTATED    4  1
  FLT1 WILD-TYPE 73 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED      4    1
  FLT1 WILD-TYPE   73   15
     clus
vv    FLT1 MUTATED FLT1 WILD-TYPE
  NO             4             73
  YES            1             15
[1] 2 2
[1] FALSE
D21V9, binary
                cls
clus              0  1
  FLT1 MUTATED    7  0
  FLT1 WILD-TYPE 99 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED      7    0
  FLT1 WILD-TYPE   99   10
                                clus
vv                               FLT1 MUTATED FLT1 WILD-TYPE
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  FLT1 MUTATED    5  0  0  0
  FLT1 WILD-TYPE 83  2  9  4
D21V10, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  R0            5             83
  R1            0              2
  R2            0              9
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous

Clustering(22) Variable = SLC12A6 MUTATION ANALYSIS
D22V1, survival
                   sevent
clus2                0  1
  SLC12A6 MUTATED    5  1
  SLC12A6 WILD-TYPE 90 20
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               110 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                1                20 
$`SLC12A6 MUTATED`
TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6547 TCGA-CI-6622 TCGA-F5-6811 
       37.97        13.02        20.98         2.50        44.78        32.19 

$`SLC12A6 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56        17.49        43.20        27.55         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17        13.78        48.20        78.12         7.17        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        42.35        28.57 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
             2.50              0.99 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            44.78            126.44 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
           26.585            24.245 
[1] "2.5 - 44.8 (26.6)"  "1.0 - 126.4 (24.2)"
[1] "hr=" "1"  
D22V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SLC12A6 MUTATED         3        0         1         1         0          0
  SLC12A6 WILD-TYPE      24        7        28         1         4          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLC12A6 MUTATED            0          0        0         0
  SLC12A6 WILD-TYPE         16         10       13         5
D22V3, multiclass
            clus
vv           SLC12A6 MUTATED SLC12A6 WILD-TYPE
  STAGE I                  3                24
  STAGE II                 0                 7
  STAGE IIA                1                28
  STAGE IIB                1                 1
  STAGE III                0                 4
  STAGE IIIA               0                 4
  STAGE IIIB               0                16
  STAGE IIIC               0                10
  STAGE IV                 0                13
  STAGE IVA                0                 5
[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
  SLC12A6 MUTATED    1  2  2  1
  SLC12A6 WILD-TYPE  7 23 78  8
D22V4, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  T1               1                 7
  T2               2                23
  T3               2                78
  T4               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  SLC12A6 MUTATED    6  0  0
  SLC12A6 WILD-TYPE 61 32 21
D22V5, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  N0               6                61
  N1               0                32
  N2               0                21
[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"
D22V6, binary
                   cls
clus                 0  1
  SLC12A6 MUTATED    4  0
  SLC12A6 WILD-TYPE 88 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED      4    0
  SLC12A6 WILD-TYPE   88   17
   clus
vv  SLC12A6 MUTATED SLC12A6 WILD-TYPE
  0               4                88
  1               0                17
[1] 2 2
[1] FALSE
D22V7, binary
                   cls
clus                 0  1
  SLC12A6 MUTATED    3  3
  SLC12A6 WILD-TYPE 52 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED      3    3
  SLC12A6 WILD-TYPE   52   64
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  FEMALE               3                52
  MALE                 3                64
[1] 2 2
[1] FALSE
D22V8, binary
                   cls
clus                 0  1
  SLC12A6 MUTATED    5  1
  SLC12A6 WILD-TYPE 72 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED      5    1
  SLC12A6 WILD-TYPE   72   15
     clus
vv    SLC12A6 MUTATED SLC12A6 WILD-TYPE
  NO                5                72
  YES               1                15
[1] 2 2
[1] FALSE
D22V9, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED     5   0
  SLC12A6 WILD-TYPE 101  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED      5    0
  SLC12A6 WILD-TYPE  101   10
                                clus
vv                               SLC12A6 MUTATED SLC12A6 WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  SLC12A6 MUTATED    2  0  0  0
  SLC12A6 WILD-TYPE 86  2  9  4
D22V10, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2               101 
       TCGA-AF-3913        TCGA-AG-3580        TCGA-AG-3611        TCGA-AG-3612 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-4008        TCGA-AG-A00H        TCGA-AG-A014 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A015        TCGA-G5-6235        TCGA-G5-6641        TCGA-AF-2687 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6655        TCGA-AG-3574 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3581        TCGA-AG-3582 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3726        TCGA-AG-3727 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-3878 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4015 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00Y        TCGA-AG-A011 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-F5-6813 
"SLC12A6 WILD-TYPE" 
D22V11, continuous

Clustering(23) Variable = AKAP9 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2              0  1
  AKAP9 MUTATED    7  0
  AKAP9 WILD-TYPE 88 21
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              7             109 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
              0              21 
$`AKAP9 MUTATED`
TCGA-AF-2693 TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02N 
       37.97        29.98        13.02        20.98        13.94        61.97 
TCGA-CL-5918 
        7.17 

$`AKAP9 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6136 
       39.48        43.04        13.55        34.49        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        24.59        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A00C 
       19.99        28.04        36.03        14.04         1.02         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         2.50 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       17.49        43.20        27.55         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       44.78        48.20        78.12        26.04        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       12.62       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         3.48        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35        28.57        32.19        36.49 
TCGA-F5-6813 
       19.66 

  AKAP9 MUTATED AKAP9 WILD-TYPE 
           7.17            0.99 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
          61.97          126.44 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
          20.98           24.36 
[1] "7.2 - 62.0 (21.0)"  "1.0 - 126.4 (24.4)"
[1] "hr="     "7.6e+07"
D23V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  AKAP9 MUTATED         4        1         1         0         0          0
  AKAP9 WILD-TYPE      23        6        28         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP9 MUTATED            0          0        0         1
  AKAP9 WILD-TYPE         16         10       13         4
D23V3, multiclass
            clus
vv           AKAP9 MUTATED AKAP9 WILD-TYPE
  STAGE I                4              23
  STAGE II               1               6
  STAGE IIA              1              28
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              1               4
[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
  AKAP9 MUTATED    1  3  2  1
  AKAP9 WILD-TYPE  7 22 78  8
D23V4, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  T1             1               7
  T2             3              22
  T3             2              78
  T4             1               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  AKAP9 MUTATED    6  0  1
  AKAP9 WILD-TYPE 61 32 20
D23V5, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  N0             6              61
  N1             0              32
  N2             1              20
[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"
D23V6, binary
                 cls
clus               0  1
  AKAP9 MUTATED    4  0
  AKAP9 WILD-TYPE 88 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED      4    0
  AKAP9 WILD-TYPE   88   17
   clus
vv  AKAP9 MUTATED AKAP9 WILD-TYPE
  0             4              88
  1             0              17
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus               0  1
  AKAP9 MUTATED    3  4
  AKAP9 WILD-TYPE 52 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED      3    4
  AKAP9 WILD-TYPE   52   63
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  FEMALE             3              52
  MALE               4              63
[1] 2 2
[1] FALSE
D23V8, binary
                 cls
clus               0  1
  AKAP9 MUTATED    6  0
  AKAP9 WILD-TYPE 71 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED      6    0
  AKAP9 WILD-TYPE   71   16
     clus
vv    AKAP9 MUTATED AKAP9 WILD-TYPE
  NO              6              71
  YES             0              16
[1] 2 2
[1] FALSE
D23V9, binary
                 cls
clus                0   1
  AKAP9 MUTATED     4   1
  AKAP9 WILD-TYPE 102   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED      4    1
  AKAP9 WILD-TYPE  102    9
                                clus
vv                               AKAP9 MUTATED AKAP9 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  AKAP9 MUTATED    5  0  0  1
  AKAP9 WILD-TYPE 83  2  9  3
D23V10, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  R0             5              83
  R1             0               2
  R2             0               9
  RX             1               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous

Clustering(24) Variable = VCX2 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2             0  1
  VCX2 MUTATED    2  3
  VCX2 WILD-TYPE 93 18
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            111 
  VCX2 MUTATED VCX2 WILD-TYPE 
             3             18 
$`VCX2 MUTATED`
TCGA-AH-6547 TCGA-CI-6619 TCGA-CL-5918 TCGA-DY-A1DD TCGA-F5-6702 
        2.50         6.05         7.17        57.24        28.57 

$`VCX2 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       43.20        27.55        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

  VCX2 MUTATED VCX2 WILD-TYPE 
          2.50           0.99 
  VCX2 MUTATED VCX2 WILD-TYPE 
         57.24         126.44 
  VCX2 MUTATED VCX2 WILD-TYPE 
          7.17          24.36 
[1] "2.5 - 57.2 (7.2)"   "1.0 - 126.4 (24.4)"
[1] "hr=" "3.6"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  VCX2 MUTATED         0        0         1         0         0          0
  VCX2 WILD-TYPE      27        7        28         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCX2 MUTATED            1          0        1         1
  VCX2 WILD-TYPE         15         10       12         4
D24V3, multiclass
            clus
vv           VCX2 MUTATED VCX2 WILD-TYPE
  STAGE I               0             27
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            1             15
  STAGE IIIC            0             10
  STAGE IV              1             12
  STAGE IVA             1              4
[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
  VCX2 MUTATED    0  0  5  0
  VCX2 WILD-TYPE  8 25 75  9
D24V4, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  T1            0              8
  T2            0             25
  T3            5             75
  T4            0              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
  VCX2 MUTATED    2  3  0
  VCX2 WILD-TYPE 65 29 21
D24V5, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  N0            2             65
  N1            3             29
  N2            0             21
[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"
D24V6, binary
                cls
clus              0  1
  VCX2 MUTATED    1  2
  VCX2 WILD-TYPE 91 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      1    2
  VCX2 WILD-TYPE   91   15
   clus
vv  VCX2 MUTATED VCX2 WILD-TYPE
  0            1             91
  1            2             15
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus              0  1
  VCX2 MUTATED    3  2
  VCX2 WILD-TYPE 52 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      3    2
  VCX2 WILD-TYPE   52   65
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  FEMALE            3             52
  MALE              2             65
[1] 2 2
[1] FALSE
D24V8, binary
                cls
clus              0  1
  VCX2 MUTATED    3  0
  VCX2 WILD-TYPE 74 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      3    0
  VCX2 WILD-TYPE   74   16
     clus
vv    VCX2 MUTATED VCX2 WILD-TYPE
  NO             3             74
  YES            0             16
[1] 2 2
[1] FALSE
D24V9, binary
                cls
clus               0   1
  VCX2 MUTATED     5   0
  VCX2 WILD-TYPE 101  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      5    0
  VCX2 WILD-TYPE  101   10
                                clus
vv                               VCX2 MUTATED VCX2 WILD-TYPE
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  VCX2 MUTATED    1  0  0  1
  VCX2 WILD-TYPE 87  2  9  3
D24V10, multiclass
[1] "Remove cluster labels:" "VCX2 MUTATED"          
clus
  VCX2 MUTATED VCX2 WILD-TYPE 
             2            101 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2687 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3581     TCGA-AG-3582 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3726     TCGA-AG-3727 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A016     TCGA-AG-A01L 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6549     TCGA-AH-6643 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-CL-5917     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6812 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-F5-6813 
"VCX2 WILD-TYPE" 
D24V11, continuous

Clustering(25) Variable = ELF3 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2             0  1
  ELF3 MUTATED    3  1
  ELF3 WILD-TYPE 92 20
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            112 
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             20 
$`ELF3 MUTATED`
TCGA-AG-3599 TCGA-AG-3892 TCGA-AG-3902 TCGA-AH-6643 
       12.03        13.02        32.02        43.20 

$`ELF3 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 
       19.99        28.04        36.03        14.04         1.02        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         2.50        17.49        27.55         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  ELF3 MUTATED ELF3 WILD-TYPE 
         12.03           0.99 
  ELF3 MUTATED ELF3 WILD-TYPE 
         43.20         126.44 
  ELF3 MUTATED ELF3 WILD-TYPE 
        22.520         24.245 
[1] "12.0 - 43.2 (22.5)" "1.0 - 126.4 (24.2)"
[1] "hr=" "1.4"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ELF3 MUTATED         2        0         1         0         0          0
  ELF3 WILD-TYPE      25        7        28         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELF3 MUTATED            0          1        0         0
  ELF3 WILD-TYPE         16          9       13         5
D25V3, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               2             25
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            0             16
  STAGE IIIC            1              9
  STAGE IV              0             13
  STAGE IVA             0              5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  ELF3 MUTATED    1  1  2  0
  ELF3 WILD-TYPE  7 24 78  9
D25V4, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  T1            1              7
  T2            1             24
  T3            2             78
  T4            0              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
  ELF3 MUTATED    3  0  1
  ELF3 WILD-TYPE 64 32 20
D25V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            3             64
  N1            0             32
  N2            1             20
[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"
D25V6, binary
                cls
clus              0  1
  ELF3 MUTATED    4  0
  ELF3 WILD-TYPE 88 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      4    0
  ELF3 WILD-TYPE   88   17
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0            4             88
  1            0             17
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus              0  1
  ELF3 MUTATED    1  3
  ELF3 WILD-TYPE 54 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      1    3
  ELF3 WILD-TYPE   54   64
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            1             54
  MALE              3             64
[1] 2 2
[1] FALSE
D25V8, binary
                cls
clus              0  1
  ELF3 MUTATED    4  0
  ELF3 WILD-TYPE 73 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      4    0
  ELF3 WILD-TYPE   73   16
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO             4             73
  YES            0             16
[1] 2 2
[1] FALSE
D25V9, binary
                cls
clus               0   1
  ELF3 MUTATED     3   0
  ELF3 WILD-TYPE 103  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      3    0
  ELF3 WILD-TYPE  103   10
                                clus
vv                               ELF3 MUTATED ELF3 WILD-TYPE
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  ELF3 MUTATED    4  0  0  0
  ELF3 WILD-TYPE 84  2  9  4
D25V10, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  R0            4             84
  R1            0              2
  R2            0              9
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous

Clustering(26) Variable = PIK3CA MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   30  5
  PIK3CA WILD-TYPE 65 16
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              35               81 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5               16 
$`PIK3CA MUTATED`
TCGA-AG-A00H TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6672 
       25.97        55.76        46.92        37.97        24.36        24.59 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3901 TCGA-AG-A020 
       37.02         0.99         0.99        36.95        25.02         1.02 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
       61.97        38.56        43.20        27.55         6.05        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
       48.20        78.12         7.17        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG 
       25.05        25.05        12.62       126.44        41.36        51.48 
TCGA-EF-5830 TCGA-EI-6507 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 
        3.48        19.96        42.35        32.19        19.66 

$`PIK3CA WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       15.95        36.03        26.43        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       34.49        29.98        16.83        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
        0.99        15.95        19.99         7.99         0.99        32.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99         1.02        17.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         9.07        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6620 
       41.00        38.04       117.11         2.50        17.49        33.17 
TCGA-CI-6621 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DD 
       13.78        26.04        13.97        44.02        25.97        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       24.13        32.61        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6812 
       49.51        28.57        36.49 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.99             0.99 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          126.44           117.11 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           31.00            20.02 
[1] "1.0 - 126.4 (31.0)" "1.0 - 117.1 (20.0)"
[1] "hr=" "2.5"
D26V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PIK3CA MUTATED         6        2        10         2         1          0
  PIK3CA WILD-TYPE      21        5        19         0         3          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIK3CA MUTATED            5          4        3         1
  PIK3CA WILD-TYPE         11          6       10         4
D26V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 6               21
  STAGE II                2                5
  STAGE IIA              10               19
  STAGE IIB               2                0
  STAGE III               1                3
  STAGE IIIA              0                4
  STAGE IIIB              5               11
  STAGE IIIC              4                6
  STAGE IV                3               10
  STAGE IVA               1                4
[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  5 26  4
  PIK3CA WILD-TYPE  7 20 54  5
D26V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1                7
  T2              5               20
  T3             26               54
  T4              4                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
  PIK3CA MUTATED   20 10  5
  PIK3CA WILD-TYPE 47 22 16
D26V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             20               47
  N1             10               22
  N2              5               16
[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"
D26V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED   25  4
  PIK3CA WILD-TYPE 67 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     25    4
  PIK3CA WILD-TYPE   67   13
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             25               67
  1              4               13
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED   13 23
  PIK3CA WILD-TYPE 42 44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     13   23
  PIK3CA WILD-TYPE   42   44
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             13               42
  MALE               23               44
[1] 2 2
[1] FALSE
D26V8, binary
                  cls
clus                0  1
  PIK3CA MUTATED   19  7
  PIK3CA WILD-TYPE 58  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     19    7
  PIK3CA WILD-TYPE   58    9
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              19               58
  YES              7                9
[1] 2 2
[1] FALSE
D26V9, binary
                  cls
clus                0  1
  PIK3CA MUTATED   31  4
  PIK3CA WILD-TYPE 75  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     31    4
  PIK3CA WILD-TYPE   75    6
                                clus
vv                               PIK3CA MUTATED PIK3CA WILD-TYPE
  RECTAL ADENOCARCINOMA                      31               75
  RECTAL MUCINOUS ADENOCARCINOMA              4                6
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  PIK3CA MUTATED   19  1  1  3
  PIK3CA WILD-TYPE 69  1  8  1
D26V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             19               69
  R1              1                1
  R2              1                8
  RX              3                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous

Clustering(27) Variable = BRAF MUTATION ANALYSIS
D27V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   11  2
  BRAF WILD-TYPE 84 19
  BRAF MUTATED BRAF WILD-TYPE 
            13            103 
  BRAF MUTATED BRAF WILD-TYPE 
             2             19 
$`BRAF MUTATED`
TCGA-AG-3578 TCGA-AG-3885 TCGA-AG-A002 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       32.02        17.95        20.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 
       25.05        12.62        57.24         3.48        20.91        18.28 
TCGA-F5-6811 
       32.19 

$`BRAF WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
        7.17        26.04        31.00        13.97        51.98        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        41.36        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
       19.96         9.96        49.51        42.35        28.57        36.49 
TCGA-F5-6813 
       19.66 

  BRAF MUTATED BRAF WILD-TYPE 
          3.48           0.99 
  BRAF MUTATED BRAF WILD-TYPE 
         57.24         126.44 
  BRAF MUTATED BRAF WILD-TYPE 
         20.98          24.36 
[1] "3.5 - 57.2 (21.0)"  "1.0 - 126.4 (24.4)"
[1] "hr=" "1.2"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BRAF MUTATED         3        1         2         1         0          0
  BRAF WILD-TYPE      24        6        27         1         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED            4          0        0         1
  BRAF WILD-TYPE         12         10       13         4
D27V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               3             24
  STAGE II              1              6
  STAGE IIA             2             27
  STAGE IIB             1              1
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            4             12
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             1              4
[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    0  4  8  1
  BRAF WILD-TYPE  8 21 72  8
D27V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            0              8
  T2            4             21
  T3            8             72
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  BRAF MUTATED    8  4  1
  BRAF WILD-TYPE 59 28 20
D27V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0            8             59
  N1            4             28
  N2            1             20
[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"
D27V6, binary
                cls
clus              0  1
  BRAF MUTATED   11  1
  BRAF WILD-TYPE 81 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11    1
  BRAF WILD-TYPE   81   16
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           11             81
  1            1             16
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus              0  1
  BRAF MUTATED    7  6
  BRAF WILD-TYPE 48 61
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      7    6
  BRAF WILD-TYPE   48   61
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            7             48
  MALE              6             61
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus              0  1
  BRAF MUTATED   10  2
  BRAF WILD-TYPE 67 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10    2
  BRAF WILD-TYPE   67   14
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            10             67
  YES            2             14
[1] 2 2
[1] FALSE
D27V9, binary
                cls
clus              0  1
  BRAF MUTATED   11  2
  BRAF WILD-TYPE 95  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11    2
  BRAF WILD-TYPE   95    8
                                clus
vv                               BRAF MUTATED BRAF WILD-TYPE
  RECTAL ADENOCARCINOMA                    11             95
  RECTAL MUCINOUS ADENOCARCINOMA            2              8
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  BRAF MUTATED   10  0  0  1
  BRAF WILD-TYPE 78  2  9  3
D27V10, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           10             78
  R1            0              2
  R2            0              9
  RX            1              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous

Clustering(28) Variable = KIAA1804 MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  KIAA1804 MUTATED    8  1
  KIAA1804 WILD-TYPE 87 20
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                107 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                 20 
$`KIAA1804 MUTATED`
TCGA-AF-2691 TCGA-AG-3582 TCGA-AG-3598 TCGA-AG-3727 TCGA-AG-3898 TCGA-AG-A002 
       43.04        36.03        50.04         0.99        48.03        20.98 
TCGA-AG-A008 TCGA-AG-A02N TCGA-EI-6508 
       13.94        61.97        20.91 

$`KIAA1804 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        13.55        37.97        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       36.03        14.04         1.02         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        9.07         1.02        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        3.48        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.99               0.99 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             61.97             126.44 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             36.03              24.13 
[1] "1.0 - 62.0 (36.0)"  "1.0 - 126.4 (24.1)"
[1] "hr=" "2.7"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KIAA1804 MUTATED         3        1         2         0         1          0
  KIAA1804 WILD-TYPE      24        6        27         2         3          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIAA1804 MUTATED            1          1        1         0
  KIAA1804 WILD-TYPE         15          9       12         5
D28V3, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   3                 24
  STAGE II                  1                  6
  STAGE IIA                 2                 27
  STAGE IIB                 0                  2
  STAGE III                 1                  3
  STAGE IIIA                0                  4
  STAGE IIIB                1                 15
  STAGE IIIC                1                  9
  STAGE IV                  1                 12
  STAGE IVA                 0                  5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  KIAA1804 MUTATED    1  2  7  0
  KIAA1804 WILD-TYPE  7 23 73  9
D28V4, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                1                  7
  T2                2                 23
  T3                7                 73
  T4                0                  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
  KIAA1804 MUTATED    6  3  1
  KIAA1804 WILD-TYPE 61 29 20
D28V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0                6                 61
  N1                3                 29
  N2                1                 20
[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"
D28V6, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    9  1
  KIAA1804 WILD-TYPE 83 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      9    1
  KIAA1804 WILD-TYPE   83   16
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0                9                 83
  1                1                 16
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    5  5
  KIAA1804 WILD-TYPE 50 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      5    5
  KIAA1804 WILD-TYPE   50   62
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE                5                 50
  MALE                  5                 62
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    7  0
  KIAA1804 WILD-TYPE 70 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      7    0
  KIAA1804 WILD-TYPE   70   16
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                 7                 70
  YES                0                 16
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    9  1
  KIAA1804 WILD-TYPE 97  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      9    1
  KIAA1804 WILD-TYPE   97    9
                                clus
vv                               KIAA1804 MUTATED KIAA1804 WILD-TYPE
  RECTAL ADENOCARCINOMA                         9                 97
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  KIAA1804 MUTATED    9  0  1  0
  KIAA1804 WILD-TYPE 79  2  8  4
D28V10, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0                9                 79
  R1                0                  2
  R2                1                  8
  RX                0                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous

Clustering(29) Variable = ERBB2 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  ERBB2 MUTATED    8  1
  ERBB2 WILD-TYPE 87 20
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             107 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              1              20 
$`ERBB2 MUTATED`
TCGA-AF-2693 TCGA-AG-3599 TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-A002 
       37.97        12.03        32.98        48.03        32.02        20.98 
TCGA-AH-6544 TCGA-AH-6644 TCGA-F5-6464 
       38.56        27.55         9.96 

$`ERBB2 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        25.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       36.03        14.04         1.02        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         2.50        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       43.20         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        3.48        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           9.96            0.99 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          48.03          126.44 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          32.02           24.00 
[1] "10.0 - 48.0 (32.0)" "1.0 - 126.4 (24.0)"
[1] "hr=" "1.6"
D29V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ERBB2 MUTATED         4        0         2         0         0          0
  ERBB2 WILD-TYPE      23        7        27         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED            0          1        0         0
  ERBB2 WILD-TYPE         16          9       13         5
D29V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                4              23
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             1               9
  STAGE IV               0              13
  STAGE IVA              0               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  ERBB2 MUTATED    0  4  4  1
  ERBB2 WILD-TYPE  8 21 76  8
D29V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0               8
  T2             4              21
  T3             4              76
  T4             1               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  ERBB2 MUTATED    6  1  1
  ERBB2 WILD-TYPE 61 31 20
D29V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             6              61
  N1             1              31
  N2             1              20
[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"
D29V6, binary
                 cls
clus               0  1
  ERBB2 MUTATED    6  1
  ERBB2 WILD-TYPE 86 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      6    1
  ERBB2 WILD-TYPE   86   16
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0             6              86
  1             1              16
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus               0  1
  ERBB2 MUTATED    2  7
  ERBB2 WILD-TYPE 53 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      2    7
  ERBB2 WILD-TYPE   53   60
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             2              53
  MALE               7              60
[1] 2 2
[1] FALSE
D29V8, binary
                 cls
clus               0  1
  ERBB2 MUTATED    9  0
  ERBB2 WILD-TYPE 68 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      9    0
  ERBB2 WILD-TYPE   68   16
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              9              68
  YES             0              16
[1] 2 2
[1] FALSE
D29V9, binary
                 cls
clus               0  1
  ERBB2 MUTATED    7  0
  ERBB2 WILD-TYPE 99 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      7    0
  ERBB2 WILD-TYPE   99   10
                                clus
vv                               ERBB2 MUTATED ERBB2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  ERBB2 MUTATED    6  0  0  0
  ERBB2 WILD-TYPE 82  2  9  4
D29V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             6              82
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous

Clustering(30) Variable = CDKL5 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  CDKL5 MUTATED    3  1
  CDKL5 WILD-TYPE 92 20
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              4             112 
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              1              20 
$`CDKL5 MUTATED`
TCGA-AF-2693 TCGA-AG-3742 TCGA-AG-A002 TCGA-DY-A1DD 
       37.97         0.99        20.98        57.24 

$`CDKL5 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  CDKL5 MUTATED CDKL5 WILD-TYPE 
           0.99            0.99 
  CDKL5 MUTATED CDKL5 WILD-TYPE 
          57.24          126.44 
  CDKL5 MUTATED CDKL5 WILD-TYPE 
         29.475          24.245 
[1] "1.0 - 57.2 (29.5)"  "1.0 - 126.4 (24.2)"
[1] "hr=" "1.1"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CDKL5 MUTATED         3        0         0         0         0          0
  CDKL5 WILD-TYPE      24        7        29         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDKL5 MUTATED            1          0        0         0
  CDKL5 WILD-TYPE         15         10       13         5
D30V3, multiclass
            clus
vv           CDKL5 MUTATED CDKL5 WILD-TYPE
  STAGE I                3              24
  STAGE II               0               7
  STAGE IIA              0              29
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             1              15
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[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
  CDKL5 MUTATED    1  2  1  0
  CDKL5 WILD-TYPE  7 23 79  9
D30V4, multiclass
    clus
vv   CDKL5 MUTATED CDKL5 WILD-TYPE
  T1             1               7
  T2             2              23
  T3             1              79
  T4             0               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
  CDKL5 MUTATED    3  1  0
  CDKL5 WILD-TYPE 64 31 21
D30V5, multiclass
    clus
vv   CDKL5 MUTATED CDKL5 WILD-TYPE
  N0             3              64
  N1             1              31
  N2             0              21
[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"
D30V6, binary
                 cls
clus               0  1
  CDKL5 MUTATED    3  0
  CDKL5 WILD-TYPE 89 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL5 MUTATED      3    0
  CDKL5 WILD-TYPE   89   17
   clus
vv  CDKL5 MUTATED CDKL5 WILD-TYPE
  0             3              89
  1             0              17
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus               0  1
  CDKL5 MUTATED    2  2
  CDKL5 WILD-TYPE 53 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL5 MUTATED      2    2
  CDKL5 WILD-TYPE   53   65
        clus
vv       CDKL5 MUTATED CDKL5 WILD-TYPE
  FEMALE             2              53
  MALE               2              65
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus               0  1
  CDKL5 MUTATED    2  0
  CDKL5 WILD-TYPE 75 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL5 MUTATED      2    0
  CDKL5 WILD-TYPE   75   16
     clus
vv    CDKL5 MUTATED CDKL5 WILD-TYPE
  NO              2              75
  YES             0              16
[1] 2 2
[1] FALSE
D30V9, binary
                 cls
clus                0   1
  CDKL5 MUTATED     3   0
  CDKL5 WILD-TYPE 103  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL5 MUTATED      3    0
  CDKL5 WILD-TYPE  103   10
                                clus
vv                               CDKL5 MUTATED CDKL5 WILD-TYPE
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  CDKL5 MUTATED    2  0  0  0
  CDKL5 WILD-TYPE 86  2  9  4
D30V10, multiclass
[1] "Remove cluster labels:" "CDKL5 MUTATED"         
clus
  CDKL5 MUTATED CDKL5 WILD-TYPE 
              2             101 
     TCGA-AF-3913      TCGA-AG-3580      TCGA-AG-3611      TCGA-AG-3612 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3890      TCGA-AG-4008      TCGA-AG-A00H      TCGA-AG-A014 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A015      TCGA-G5-6235      TCGA-G5-6641      TCGA-AF-2687 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6655      TCGA-AG-3574 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3581      TCGA-AG-3582 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3726      TCGA-AG-3727 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3878      TCGA-AG-3882 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3892 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4015 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00Y      TCGA-AG-A011 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" "CDKL5 WILD-TYPE" 
     TCGA-F5-6813 
"CDKL5 WILD-TYPE" 
D30V11, continuous

Clustering(31) Variable = ZNF354C MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  ZNF354C MUTATED    4  1
  ZNF354C WILD-TYPE 91 20
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               111 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                1                20 
$`ZNF354C MUTATED`
TCGA-AG-A002 TCGA-AH-6544 TCGA-EI-6507 TCGA-F5-6465 TCGA-F5-6813 
       20.98        38.56        19.96        49.51        19.66 

$`ZNF354C WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       14.04         1.02        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
        3.48        20.55        20.91        18.28         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       28.57        32.19        36.49 

  ZNF354C MUTATED ZNF354C WILD-TYPE 
            19.66              0.99 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            49.51            126.44 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            20.98             24.36 
[1] "19.7 - 49.5 (21.0)" "1.0 - 126.4 (24.4)"
[1] "hr=" "1.1"
D31V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ZNF354C MUTATED         1        0         2         0         0          0
  ZNF354C WILD-TYPE      26        7        27         2         4          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF354C MUTATED            0          1        0         0
  ZNF354C WILD-TYPE         16          9       13         5
D31V3, multiclass
            clus
vv           ZNF354C MUTATED ZNF354C WILD-TYPE
  STAGE I                  1                26
  STAGE II                 0                 7
  STAGE IIA                2                27
  STAGE IIB                0                 2
  STAGE III                0                 4
  STAGE IIIA               0                 4
  STAGE IIIB               0                16
  STAGE IIIC               1                 9
  STAGE IV                 0                13
  STAGE IVA                0                 5
[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
  ZNF354C MUTATED    0  1  3  1
  ZNF354C WILD-TYPE  8 24 77  8
D31V4, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  T1               0                 8
  T2               1                24
  T3               3                77
  T4               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  ZNF354C MUTATED    3  1  1
  ZNF354C WILD-TYPE 64 31 20
D31V5, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  N0               3                64
  N1               1                31
  N2               1                20
[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"
D31V6, binary
                   cls
clus                 0  1
  ZNF354C MUTATED    4  1
  ZNF354C WILD-TYPE 88 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      4    1
  ZNF354C WILD-TYPE   88   16
   clus
vv  ZNF354C MUTATED ZNF354C WILD-TYPE
  0               4                88
  1               1                16
[1] 2 2
[1] FALSE
D31V7, binary
                   cls
clus                 0  1
  ZNF354C MUTATED    1  4
  ZNF354C WILD-TYPE 54 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      1    4
  ZNF354C WILD-TYPE   54   63
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  FEMALE               1                54
  MALE                 4                63
[1] 2 2
[1] FALSE
D31V8, binary
                   cls
clus                 0  1
  ZNF354C MUTATED    5  0
  ZNF354C WILD-TYPE 72 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      5    0
  ZNF354C WILD-TYPE   72   16
     clus
vv    ZNF354C MUTATED ZNF354C WILD-TYPE
  NO                5                72
  YES               0                16
[1] 2 2
[1] FALSE
D31V9, binary
                   cls
clus                  0   1
  ZNF354C MUTATED     5   0
  ZNF354C WILD-TYPE 101  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      5    0
  ZNF354C WILD-TYPE  101   10
                                clus
vv                               ZNF354C MUTATED ZNF354C WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  ZNF354C MUTATED    4  0  0  0
  ZNF354C WILD-TYPE 84  2  9  4
D31V10, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  R0               4                84
  R1               0                 2
  R2               0                 9
  RX               0                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous

Clustering(32) Variable = LIG1 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2             0  1
  LIG1 MUTATED    4  0
  LIG1 WILD-TYPE 91 21
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            112 
  LIG1 MUTATED LIG1 WILD-TYPE 
             0             21 
$`LIG1 MUTATED`
TCGA-AG-3732 TCGA-DC-6155 TCGA-EI-6507 TCGA-EI-6510 
       32.98        13.97        19.96        18.28 

$`LIG1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 
       48.20        78.12         7.17        26.04        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
        3.48        20.55        20.91         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  LIG1 MUTATED LIG1 WILD-TYPE 
         13.97           0.99 
  LIG1 MUTATED LIG1 WILD-TYPE 
         32.98         126.44 
  LIG1 MUTATED LIG1 WILD-TYPE 
        19.120         24.475 
[1] "14.0 - 33.0 (19.1)" "1.0 - 126.4 (24.5)"
[1] "hr="     "9400000"
D32V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  LIG1 MUTATED         1        0         1         0         0          1
  LIG1 WILD-TYPE      26        7        28         2         4          3
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIG1 MUTATED            0          0        0         0
  LIG1 WILD-TYPE         16         10       13         5
D32V3, multiclass
            clus
vv           LIG1 MUTATED LIG1 WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            1              3
  STAGE IIIB            0             16
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             0              5
[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
  LIG1 MUTATED    0  3  1  0
  LIG1 WILD-TYPE  8 22 79  9
D32V4, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  T1            0              8
  T2            3             22
  T3            1             79
  T4            0              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
  LIG1 MUTATED    3  1  0
  LIG1 WILD-TYPE 64 31 21
D32V5, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  N0            3             64
  N1            1             31
  N2            0             21
[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"
D32V6, binary
                cls
clus              0  1
  LIG1 MUTATED    3  0
  LIG1 WILD-TYPE 89 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      3    0
  LIG1 WILD-TYPE   89   17
   clus
vv  LIG1 MUTATED LIG1 WILD-TYPE
  0            3             89
  1            0             17
[1] 2 2
[1] FALSE
D32V7, binary
                cls
clus              0  1
  LIG1 MUTATED    3  1
  LIG1 WILD-TYPE 52 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      3    1
  LIG1 WILD-TYPE   52   66
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  FEMALE            3             52
  MALE              1             66
[1] 2 2
[1] FALSE
D32V8, binary
                cls
clus              0  1
  LIG1 MUTATED    4  0
  LIG1 WILD-TYPE 73 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      4    0
  LIG1 WILD-TYPE   73   16
     clus
vv    LIG1 MUTATED LIG1 WILD-TYPE
  NO             4             73
  YES            0             16
[1] 2 2
[1] FALSE
D32V9, binary
                cls
clus               0   1
  LIG1 MUTATED     4   0
  LIG1 WILD-TYPE 102  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      4    0
  LIG1 WILD-TYPE  102   10
                                clus
vv                               LIG1 MUTATED LIG1 WILD-TYPE
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  LIG1 MUTATED    4  0  0  0
  LIG1 WILD-TYPE 84  2  9  4
D32V10, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  R0            4             84
  R1            0              2
  R2            0              9
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous

Clustering(33) Variable = IQCD MUTATION ANALYSIS
D33V1, survival
                sevent
clus2             0  1
  IQCD MUTATED    2  1
  IQCD WILD-TYPE 93 20
  IQCD MUTATED IQCD WILD-TYPE 
             3            113 
  IQCD MUTATED IQCD WILD-TYPE 
             1             20 
$`IQCD MUTATED`
TCGA-AF-4110 TCGA-AG-A002 TCGA-AH-6643 
       29.98        20.98        43.20 

$`IQCD WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       39.48        43.04        13.55        37.97        34.49        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        1.02        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         2.50        17.49        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

  IQCD MUTATED IQCD WILD-TYPE 
         20.98           0.99 
  IQCD MUTATED IQCD WILD-TYPE 
         43.20         126.44 
  IQCD MUTATED IQCD WILD-TYPE 
         29.98          24.13 
[1] "21.0 - 43.2 (30.0)" "1.0 - 126.4 (24.1)"
[1] "hr=" "1.5"
D33V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  IQCD MUTATED         1        0         0         0         0          0
  IQCD WILD-TYPE      26        7        29         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IQCD MUTATED            0          1        0         1
  IQCD WILD-TYPE         16          9       13         4
D33V3, multiclass
            clus
vv           IQCD MUTATED IQCD WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             0             29
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            0             16
  STAGE IIIC            1              9
  STAGE IV              0             13
  STAGE IVA             1              4
[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
  IQCD MUTATED    0  1  1  1
  IQCD WILD-TYPE  8 24 79  8
D33V4, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  T1            0              8
  T2            1             24
  T3            1             79
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  IQCD MUTATED    1  0  2
  IQCD WILD-TYPE 66 32 19
D33V5, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  N0            1             66
  N1            0             32
  N2            2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                cls
clus              0  1
  IQCD MUTATED    2  0
  IQCD WILD-TYPE 90 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      2    0
  IQCD WILD-TYPE   90   17
   clus
vv  IQCD MUTATED IQCD WILD-TYPE
  0            2             90
  1            0             17
[1] 2 2
[1] FALSE
D33V7, binary
                cls
clus              0  1
  IQCD MUTATED    0  3
  IQCD WILD-TYPE 55 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      0    3
  IQCD WILD-TYPE   55   64
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  FEMALE            0             55
  MALE              3             64
[1] 2 2
[1] FALSE
D33V8, binary
                cls
clus              0  1
  IQCD MUTATED    3  0
  IQCD WILD-TYPE 74 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      3    0
  IQCD WILD-TYPE   74   16
     clus
vv    IQCD MUTATED IQCD WILD-TYPE
  NO             3             74
  YES            0             16
[1] 2 2
[1] FALSE
D33V9, binary
                cls
clus               0   1
  IQCD MUTATED     2   0
  IQCD WILD-TYPE 104  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      2    0
  IQCD WILD-TYPE  104   10
                                clus
vv                               IQCD MUTATED IQCD WILD-TYPE
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  IQCD MUTATED    3  0  0  0
  IQCD WILD-TYPE 85  2  9  4
D33V10, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  R0            3             85
  R1            0              2
  R2            0              9
  RX            0              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous

Clustering(34) Variable = ZBED4 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2              0  1
  ZBED4 MUTATED    4  0
  ZBED4 WILD-TYPE 91 21
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              4             112 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              0              21 
$`ZBED4 MUTATED`
TCGA-AG-3581 TCGA-AG-A02N TCGA-EI-6506 TCGA-F5-6811 
        7.07        61.97        20.55        32.19 

$`ZBED4 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        9.07         1.02        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        3.48        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        36.49        19.66 

  ZBED4 MUTATED ZBED4 WILD-TYPE 
           7.07            0.99 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
          61.97          126.44 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
         26.370          24.245 
[1] "7.1 - 62.0 (26.4)"  "1.0 - 126.4 (24.2)"
[1] "hr="     "2.8e+07"
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ZBED4 MUTATED         1        1         2         0         0          0
  ZBED4 WILD-TYPE      26        6        27         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZBED4 MUTATED            0          0        0         0
  ZBED4 WILD-TYPE         16         10       13         5
D34V3, multiclass
            clus
vv           ZBED4 MUTATED ZBED4 WILD-TYPE
  STAGE I                1              26
  STAGE II               1               6
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             0              16
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               5
[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
  ZBED4 MUTATED    0  1  3  0
  ZBED4 WILD-TYPE  8 24 77  9
D34V4, multiclass
    clus
vv   ZBED4 MUTATED ZBED4 WILD-TYPE
  T1             0               8
  T2             1              24
  T3             3              77
  T4             0               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
  ZBED4 MUTATED    4  0  0
  ZBED4 WILD-TYPE 63 32 21
D34V5, multiclass
    clus
vv   ZBED4 MUTATED ZBED4 WILD-TYPE
  N0             4              63
  N1             0              32
  N2             0              21
[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"
D34V6, binary
                 cls
clus               0  1
  ZBED4 MUTATED    4  0
  ZBED4 WILD-TYPE 88 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      4    0
  ZBED4 WILD-TYPE   88   17
   clus
vv  ZBED4 MUTATED ZBED4 WILD-TYPE
  0             4              88
  1             0              17
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus               0  1
  ZBED4 MUTATED    2  2
  ZBED4 WILD-TYPE 53 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      2    2
  ZBED4 WILD-TYPE   53   65
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  FEMALE             2              53
  MALE               2              65
[1] 2 2
[1] FALSE
D34V8, binary
                 cls
clus               0  1
  ZBED4 MUTATED    3  0
  ZBED4 WILD-TYPE 74 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      3    0
  ZBED4 WILD-TYPE   74   16
     clus
vv    ZBED4 MUTATED ZBED4 WILD-TYPE
  NO              3              74
  YES             0              16
[1] 2 2
[1] FALSE
D34V9, binary
                 cls
clus                0   1
  ZBED4 MUTATED     4   0
  ZBED4 WILD-TYPE 102  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      4    0
  ZBED4 WILD-TYPE  102   10
                                clus
vv                               ZBED4 MUTATED ZBED4 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  ZBED4 MUTATED    3  0  0  0
  ZBED4 WILD-TYPE 85  2  9  4
D34V10, multiclass
    clus
vv   ZBED4 MUTATED ZBED4 WILD-TYPE
  R0             3              85
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous

Clustering(35) Variable = GMCL1 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  GMCL1 MUTATED    3  1
  GMCL1 WILD-TYPE 92 20
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              4             112 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              1              20 
$`GMCL1 MUTATED`
TCGA-AG-A002 TCGA-AH-6643 TCGA-DC-6683 TCGA-F5-6465 
       20.98        43.20        25.05        49.51 

$`GMCL1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       14.04         1.02        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  GMCL1 MUTATED GMCL1 WILD-TYPE 
          20.98            0.99 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
          49.51          126.44 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         34.125          24.065 
[1] "21.0 - 49.5 (34.1)" "1.0 - 126.4 (24.1)"
[1] "hr=" "1.1"
D35V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  GMCL1 MUTATED         1        0         1         0         0          0
  GMCL1 WILD-TYPE      26        7        28         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMCL1 MUTATED            1          1        0         0
  GMCL1 WILD-TYPE         15          9       13         5
D35V3, multiclass
            clus
vv           GMCL1 MUTATED GMCL1 WILD-TYPE
  STAGE I                1              26
  STAGE II               0               7
  STAGE IIA              1              28
  STAGE IIB              0               2
  STAGE III              0               4
  STAGE IIIA             0               4
  STAGE IIIB             1              15
  STAGE IIIC             1               9
  STAGE IV               0              13
  STAGE IVA              0               5
[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
  GMCL1 MUTATED    0  1  3  0
  GMCL1 WILD-TYPE  8 24 77  9
D35V4, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  T1             0               8
  T2             1              24
  T3             3              77
  T4             0               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
  GMCL1 MUTATED    2  1  1
  GMCL1 WILD-TYPE 65 31 20
D35V5, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  N0             2              65
  N1             1              31
  N2             1              20
[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"
D35V6, binary
                 cls
clus               0  1
  GMCL1 MUTATED    4  0
  GMCL1 WILD-TYPE 88 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      4    0
  GMCL1 WILD-TYPE   88   17
   clus
vv  GMCL1 MUTATED GMCL1 WILD-TYPE
  0             4              88
  1             0              17
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus               0  1
  GMCL1 MUTATED    1  3
  GMCL1 WILD-TYPE 54 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      1    3
  GMCL1 WILD-TYPE   54   64
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  FEMALE             1              54
  MALE               3              64
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus               0  1
  GMCL1 MUTATED    4  0
  GMCL1 WILD-TYPE 73 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      4    0
  GMCL1 WILD-TYPE   73   16
     clus
vv    GMCL1 MUTATED GMCL1 WILD-TYPE
  NO              4              73
  YES             0              16
[1] 2 2
[1] FALSE
D35V9, binary
                 cls
clus                0   1
  GMCL1 MUTATED     4   0
  GMCL1 WILD-TYPE 102  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      4    0
  GMCL1 WILD-TYPE  102   10
                                clus
vv                               GMCL1 MUTATED GMCL1 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  GMCL1 MUTATED    4  0  0  0
  GMCL1 WILD-TYPE 84  2  9  4
D35V10, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  R0             4              84
  R1             0               2
  R2             0               9
  RX             0               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous

Clustering(36) Variable = CIR1 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2             0  1
  CIR1 MUTATED    2  1
  CIR1 WILD-TYPE 93 20
  CIR1 MUTATED CIR1 WILD-TYPE 
             3            113 
  CIR1 MUTATED CIR1 WILD-TYPE 
             1             20 
$`CIR1 MUTATED`
TCGA-AF-2693 TCGA-DC-5337 TCGA-DY-A1DD 
       37.97        26.04        57.24 

$`CIR1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         2.50        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       48.20        78.12         7.17        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

  CIR1 MUTATED CIR1 WILD-TYPE 
         26.04           0.99 
  CIR1 MUTATED CIR1 WILD-TYPE 
         57.24         126.44 
  CIR1 MUTATED CIR1 WILD-TYPE 
         37.97          24.00 
[1] "26.0 - 57.2 (38.0)" "1.0 - 126.4 (24.0)"
[1] "hr=" "1.1"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CIR1 MUTATED         2        0         0         0         0          0
  CIR1 WILD-TYPE      25        7        29         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIR1 MUTATED            1          0        0         0
  CIR1 WILD-TYPE         15         10       13         5
D36V3, multiclass
            clus
vv           CIR1 MUTATED CIR1 WILD-TYPE
  STAGE I               2             25
  STAGE II              0              7
  STAGE IIA             0             29
  STAGE IIB             0              2
  STAGE III             0              4
  STAGE IIIA            0              4
  STAGE IIIB            1             15
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             0              5
[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
  CIR1 MUTATED    1  1  1  0
  CIR1 WILD-TYPE  7 24 79  9
D36V4, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  T1            1              7
  T2            1             24
  T3            1             79
  T4            0              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
  CIR1 MUTATED    2  1  0
  CIR1 WILD-TYPE 65 31 21
D36V5, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  N0            2             65
  N1            1             31
  N2            0             21
[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"
D36V6, binary
                cls
clus              0  1
  CIR1 MUTATED    2  0
  CIR1 WILD-TYPE 90 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    0
  CIR1 WILD-TYPE   90   17
   clus
vv  CIR1 MUTATED CIR1 WILD-TYPE
  0            2             90
  1            0             17
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus              0  1
  CIR1 MUTATED    1  2
  CIR1 WILD-TYPE 54 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      1    2
  CIR1 WILD-TYPE   54   65
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  FEMALE            1             54
  MALE              2             65
[1] 2 2
[1] FALSE
D36V8, binary
                cls
clus              0  1
  CIR1 MUTATED    2  0
  CIR1 WILD-TYPE 75 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    0
  CIR1 WILD-TYPE   75   16
     clus
vv    CIR1 MUTATED CIR1 WILD-TYPE
  NO             2             75
  YES            0             16
[1] 2 2
[1] FALSE
D36V9, binary
                cls
clus               0   1
  CIR1 MUTATED     2   0
  CIR1 WILD-TYPE 104  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    0
  CIR1 WILD-TYPE  104   10
                                clus
vv                               CIR1 MUTATED CIR1 WILD-TYPE
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  CIR1 MUTATED    1  0  0  0
  CIR1 WILD-TYPE 87  2  9  4
D36V10, multiclass
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             1            102 
    TCGA-AF-3913     TCGA-AG-3580     TCGA-AG-3611     TCGA-AG-3612 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-4008     TCGA-AG-A00H     TCGA-AG-A014 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A015     TCGA-G5-6235     TCGA-G5-6641     TCGA-AF-2687 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3581     TCGA-AG-3582 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3726     TCGA-AG-3727 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A016     TCGA-AG-A01L 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6549     TCGA-AH-6643 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5869     TCGA-DC-6155 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
D36V11, continuous

Clustering(37) Variable = AGL MUTATION ANALYSIS
D37V1, survival
               sevent
clus2            0  1
  AGL MUTATED    4  0
  AGL WILD-TYPE 91 21
  AGL MUTATED AGL WILD-TYPE 
            4           112 
  AGL MUTATED AGL WILD-TYPE 
            0            21 
$`AGL MUTATED`
TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-A002 TCGA-EI-6507 
       37.02        17.95        20.98        19.96 

$`AGL WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
        0.99        15.95        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         2.50        17.49        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        26.04        31.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  AGL MUTATED AGL WILD-TYPE 
        17.95          0.99 
  AGL MUTATED AGL WILD-TYPE 
        37.02        126.44 
  AGL MUTATED AGL WILD-TYPE 
       20.470        24.475 
[1] "17.9 - 37.0 (20.5)" "1.0 - 126.4 (24.5)"
[1] "hr="     "2.6e+07"
D37V2, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  AGL MUTATED         1        0         1         0         0          0
  AGL WILD-TYPE      26        7        28         2         4          4
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGL MUTATED            1          0        1         0
  AGL WILD-TYPE         15         10       12         5
D37V3, multiclass
            clus
vv           AGL MUTATED AGL WILD-TYPE
  STAGE I              1            26
  STAGE II             0             7
  STAGE IIA            1            28
  STAGE IIB            0             2
  STAGE III            0             4
  STAGE IIIA           0             4
  STAGE IIIB           1            15
  STAGE IIIC           0            10
  STAGE IV             1            12
  STAGE IVA            0             5
[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
  AGL MUTATED    0  1  3  0
  AGL WILD-TYPE  8 24 77  9
D37V4, multiclass
    clus
vv   AGL MUTATED AGL WILD-TYPE
  T1           0             8
  T2           1            24
  T3           3            77
  T4           0             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
  AGL MUTATED    2  2  0
  AGL WILD-TYPE 65 30 21
D37V5, multiclass
    clus
vv   AGL MUTATED AGL WILD-TYPE
  N0           2            65
  N1           2            30
  N2           0            21
[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"
D37V6, binary
               cls
clus             0  1
  AGL MUTATED    3  1
  AGL WILD-TYPE 89 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGL MUTATED      3    1
  AGL WILD-TYPE   89   16
   clus
vv  AGL MUTATED AGL WILD-TYPE
  0           3            89
  1           1            16
[1] 2 2
[1] FALSE
D37V7, binary
               cls
clus             0  1
  AGL MUTATED    1  3
  AGL WILD-TYPE 54 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGL MUTATED      1    3
  AGL WILD-TYPE   54   64
        clus
vv       AGL MUTATED AGL WILD-TYPE
  FEMALE           1            54
  MALE             3            64
[1] 2 2
[1] FALSE
D37V8, binary
               cls
clus             0  1
  AGL MUTATED    3  1
  AGL WILD-TYPE 74 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGL MUTATED      3    1
  AGL WILD-TYPE   74   15
     clus
vv    AGL MUTATED AGL WILD-TYPE
  NO            3            74
  YES           1            15
[1] 2 2
[1] FALSE
D37V9, binary
               cls
clus              0   1
  AGL MUTATED     4   0
  AGL WILD-TYPE 102  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGL MUTATED      4    0
  AGL WILD-TYPE  102   10
                                clus
vv                               AGL MUTATED AGL WILD-TYPE
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2 RX
  AGL MUTATED    3  0  1  0
  AGL WILD-TYPE 85  2  8  4
D37V10, multiclass
    clus
vv   AGL MUTATED AGL WILD-TYPE
  R0           3            85
  R1           0             2
  R2           1             8
  RX           0             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous

Clustering(38) Variable = FAM123B MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  FAM123B MUTATED    6  4
  FAM123B WILD-TYPE 89 17
  FAM123B MUTATED FAM123B WILD-TYPE 
               10               106 
  FAM123B MUTATED FAM123B WILD-TYPE 
                4                17 
$`FAM123B MUTATED`
TCGA-AG-3584 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A02G TCGA-AG-A02N 
       24.00        13.02         1.02        20.98        38.96        61.97 
TCGA-AH-6544 TCGA-AH-6644 TCGA-DY-A1DD TCGA-DY-A1DF 
       38.56        27.55        57.24        24.13 

$`FAM123B WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       36.95        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 
       19.99        28.04        36.03        14.04         1.02        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         9.07         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
        1.94        41.00        38.04       117.11         2.50        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       43.20         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      126.44        41.36        51.48        32.61         3.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57        32.19        36.49        19.66 

  FAM123B MUTATED FAM123B WILD-TYPE 
             1.02              0.99 
  FAM123B MUTATED FAM123B WILD-TYPE 
            61.97            126.44 
  FAM123B MUTATED FAM123B WILD-TYPE 
           25.840            23.685 
[1] "1.0 - 62.0 (25.8)"  "1.0 - 126.4 (23.7)"
[1] "hr=" "1.7"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FAM123B MUTATED         3        1         0         0         0          0
  FAM123B WILD-TYPE      24        6        29         2         4          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM123B MUTATED            1          1        2         0
  FAM123B WILD-TYPE         15          9       11         5
D38V3, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  3                24
  STAGE II                 1                 6
  STAGE IIA                0                29
  STAGE IIB                0                 2
  STAGE III                0                 4
  STAGE IIIA               0                 4
  STAGE IIIB               1                15
  STAGE IIIC               1                 9
  STAGE IV                 2                11
  STAGE IVA                0                 5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  FAM123B MUTATED    1  3  6  0
  FAM123B WILD-TYPE  7 22 74  9
D38V4, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               1                 7
  T2               3                22
  T3               6                74
  T4               0                 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
  FAM123B MUTATED    4  3  2
  FAM123B WILD-TYPE 63 29 19
D38V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0               4                63
  N1               3                29
  N2               2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                   cls
clus                 0  1
  FAM123B MUTATED    6  3
  FAM123B WILD-TYPE 86 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      6    3
  FAM123B WILD-TYPE   86   14
   clus
vv  FAM123B MUTATED FAM123B WILD-TYPE
  0               6                86
  1               3                14
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  FAM123B MUTATED    4  6
  FAM123B WILD-TYPE 51 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      4    6
  FAM123B WILD-TYPE   51   61
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE               4                51
  MALE                 6                61
[1] 2 2
[1] FALSE
D38V8, binary
                   cls
clus                 0  1
  FAM123B MUTATED    6  0
  FAM123B WILD-TYPE 71 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      6    0
  FAM123B WILD-TYPE   71   16
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  NO                6                71
  YES               0                16
[1] 2 2
[1] FALSE
D38V9, binary
                   cls
clus                 0  1
  FAM123B MUTATED   10  0
  FAM123B WILD-TYPE 96 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     10    0
  FAM123B WILD-TYPE   96   10
                                clus
vv                               FAM123B MUTATED FAM123B WILD-TYPE
  RECTAL ADENOCARCINOMA                       10                96
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  FAM123B MUTATED    4  0  2  0
  FAM123B WILD-TYPE 84  2  7  4
D38V10, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0               4                84
  R1               0                 2
  R2               2                 7
  RX               0                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous

Clustering(39) Variable = VANGL1 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2               0  1
  VANGL1 MUTATED    2  1
  VANGL1 WILD-TYPE 93 20
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              113 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               1               20 
$`VANGL1 MUTATED`
TCGA-AF-5654 TCGA-AG-3731 TCGA-F5-6465 
       16.83        37.02        49.51 

$`VANGL1 WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.36        20.02        24.59        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       15.95        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         2.50        17.49        43.20 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       27.55         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        3.48        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

  VANGL1 MUTATED VANGL1 WILD-TYPE 
           16.83             0.99 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
           49.51           126.44 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
           37.02            24.13 
[1] "16.8 - 49.5 (37.0)" "1.0 - 126.4 (24.1)"
[1] "hr=" "1.4"
D39V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  VANGL1 MUTATED         1        0         1         0         0          0
  VANGL1 WILD-TYPE      26        7        28         2         4          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VANGL1 MUTATED            0          0        1         0
  VANGL1 WILD-TYPE         16         10       12         5
D39V3, multiclass
            clus
vv           VANGL1 MUTATED VANGL1 WILD-TYPE
  STAGE I                 1               26
  STAGE II                0                7
  STAGE IIA               1               28
  STAGE IIB               0                2
  STAGE III               0                4
  STAGE IIIA              0                4
  STAGE IIIB              0               16
  STAGE IIIC              0               10
  STAGE IV                1               12
  STAGE IVA               0                5
[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
  VANGL1 MUTATED    0  1  2  0
  VANGL1 WILD-TYPE  8 24 78  9
D39V4, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  T1              0                8
  T2              1               24
  T3              2               78
  T4              0                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
  VANGL1 MUTATED    2  1  0
  VANGL1 WILD-TYPE 65 31 21
D39V5, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  N0              2               65
  N1              1               31
  N2              0               21
[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"
D39V6, binary
                  cls
clus                0  1
  VANGL1 MUTATED    2  1
  VANGL1 WILD-TYPE 90 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      2    1
  VANGL1 WILD-TYPE   90   16
   clus
vv  VANGL1 MUTATED VANGL1 WILD-TYPE
  0              2               90
  1              1               16
[1] 2 2
[1] FALSE
D39V7, binary
                  cls
clus                0  1
  VANGL1 MUTATED    2  1
  VANGL1 WILD-TYPE 53 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      2    1
  VANGL1 WILD-TYPE   53   66
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  FEMALE              2               53
  MALE                1               66
[1] 2 2
[1] FALSE
D39V8, binary
                  cls
clus                0  1
  VANGL1 MUTATED    3  0
  VANGL1 WILD-TYPE 74 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      3    0
  VANGL1 WILD-TYPE   74   16
     clus
vv    VANGL1 MUTATED VANGL1 WILD-TYPE
  NO               3               74
  YES              0               16
[1] 2 2
[1] FALSE
D39V9, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     3   0
  VANGL1 WILD-TYPE 103  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      3    0
  VANGL1 WILD-TYPE  103   10
                                clus
vv                               VANGL1 MUTATED VANGL1 WILD-TYPE
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  VANGL1 MUTATED    2  0  1  0
  VANGL1 WILD-TYPE 86  2  8  4
D39V10, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  R0              2               86
  R1              0                2
  R2              1                8
  RX              0                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous

Clustering(40) Variable = CREBBP MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2               0  1
  CREBBP MUTATED    9  1
  CREBBP WILD-TYPE 86 20
  CREBBP MUTATED CREBBP WILD-TYPE 
              10              106 
  CREBBP MUTATED CREBBP WILD-TYPE 
               1               20 
$`CREBBP MUTATED`
TCGA-AG-3731 TCGA-AG-A002 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 
       37.02        20.98        61.97        38.56        17.49        43.20 
TCGA-CI-6620 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6812 
       33.17        19.96        18.28        36.49 

$`CREBBP WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        15.95        36.03        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        24.36        20.02        24.59        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
        0.99        15.95        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        1.02        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 
      117.11         2.50        27.55         6.05        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       48.20        78.12         7.17        26.04        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       12.62       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
       32.61         3.48        20.55        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       42.35        28.57        32.19        19.66 

  CREBBP MUTATED CREBBP WILD-TYPE 
           17.49             0.99 
  CREBBP MUTATED CREBBP WILD-TYPE 
           61.97           126.44 
  CREBBP MUTATED CREBBP WILD-TYPE 
          34.830           24.065 
[1] "17.5 - 62.0 (34.8)" "1.0 - 126.4 (24.1)"
[1] "hr=" "2.6"
D40V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CREBBP MUTATED         1        1         2         0         0          0
  CREBBP WILD-TYPE      26        6        27         2         4          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CREBBP MUTATED            0          1        1         1
  CREBBP WILD-TYPE         16          9       12         4
D40V3, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                 1               26
  STAGE II                1                6
  STAGE IIA               2               27
  STAGE IIB               0                2
  STAGE III               0                4
  STAGE IIIA              0                4
  STAGE IIIB              0               16
  STAGE IIIC              1                9
  STAGE IV                1               12
  STAGE IVA               1                4
[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
  CREBBP MUTATED    0  2  8  0
  CREBBP WILD-TYPE  8 23 72  9
D40V4, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  T1              0                8
  T2              2               23
  T3              8               72
  T4              0                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
  CREBBP MUTATED    5  3  1
  CREBBP WILD-TYPE 62 29 20
D40V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0              5               62
  N1              3               29
  N2              1               20
[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"
D40V6, binary
                  cls
clus                0  1
  CREBBP MUTATED    5  3
  CREBBP WILD-TYPE 87 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      5    3
  CREBBP WILD-TYPE   87   14
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0              5               87
  1              3               14
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                0  1
  CREBBP MUTATED    2  8
  CREBBP WILD-TYPE 53 59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      2    8
  CREBBP WILD-TYPE   53   59
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE              2               53
  MALE                8               59
[1] 2 2
[1] FALSE
D40V8, binary
                  cls
clus                0  1
  CREBBP MUTATED    9  0
  CREBBP WILD-TYPE 68 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      9    0
  CREBBP WILD-TYPE   68   16
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO               9               68
  YES              0               16
[1] 2 2
[1] FALSE
D40V9, binary
                  cls
clus                0  1
  CREBBP MUTATED   10  0
  CREBBP WILD-TYPE 96 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     10    0
  CREBBP WILD-TYPE   96   10
                                clus
vv                               CREBBP MUTATED CREBBP WILD-TYPE
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  CREBBP MUTATED    6  0  1  1
  CREBBP WILD-TYPE 82  2  8  3
D40V10, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  R0              6               82
  R1              0                2
  R2              1                8
  RX              1                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
