[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/15087528/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/15178180/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=122, common to both=122
[1] "Reduce the number of clustering variables from 40 to 39."
[1]  39 122
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          106            16 
  APC MUTATED APC WILD-TYPE 
          106            16 
[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 
            90             32 
  TP53 MUTATED TP53 WILD-TYPE 
            90             32 
[1] "MUC4 MUTATION ANALYSIS"
[1] 3
  MUC4 MUTATED MUC4 WILD-TYPE 
            25             97 
  MUC4 MUTATED MUC4 WILD-TYPE 
            25             97 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              13              109 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              13              109 
[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] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            11            111 
  NRAS MUTATED NRAS 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] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              111 
[1] "RBM38 MUTATION ANALYSIS"
[1] 3
  RBM38 MUTATED RBM38 WILD-TYPE 
              8             114 
  RBM38 MUTATED RBM38 WILD-TYPE 
              8             114 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              7             115 
  SMAD2 MUTATED SMAD2 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] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             114 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             114 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              5             117 
  RBM10 MUTATED RBM10 WILD-TYPE 
              5             117 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
  PON3 MUTATED PON3 WILD-TYPE 
             4            118 
[1] "HIST2H2AC MUTATION ANALYSIS"
[1] 3
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  3                 119 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  3                 119 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              103 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                10                112 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
  OXSM MUTATED OXSM WILD-TYPE 
             4            118 
[1] "BCL9 MUTATION ANALYSIS"
[1] 3
  BCL9 MUTATED BCL9 WILD-TYPE 
             5            117 
  BCL9 MUTATED BCL9 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] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               116 
[1] "ZNF354C MUTATION ANALYSIS"
[1] 3
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               117 
[1] "GABRP MUTATION ANALYSIS"
[1] 3
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
  GABRP MUTATED GABRP WILD-TYPE 
              4             118 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            12            110 
  BRAF MUTATED BRAF WILD-TYPE 
            12            110 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              37               85 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              37               85 
[1] "CEP290 MUTATION ANALYSIS"
[1] 3
  CEP290 MUTATED CEP290 WILD-TYPE 
               6              116 
  CEP290 MUTATED CEP290 WILD-TYPE 
               6              116 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            118 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             118 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             118 
[1] "ATP8B1 MUTATION ANALYSIS"
[1] 3
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               5              117 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               5              117 
[1] "FLT1 MUTATION ANALYSIS"
[1] 3
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            114 
[1] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
             13             109 
  OBSCN MUTATED OBSCN WILD-TYPE 
             13             109 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              119 
[1] "RRP8 MUTATION ANALYSIS"
[1] 3
  RRP8 MUTATED RRP8 WILD-TYPE 
             5            117 
  RRP8 MUTATED RRP8 WILD-TYPE 
             5            117 
[1] "AGL MUTATION ANALYSIS"
[1] 3
  AGL MUTATED AGL WILD-TYPE 
            4           118 
  AGL MUTATED AGL WILD-TYPE 
            4           118 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
             3            119 
  RLIM MUTATED RLIM WILD-TYPE 
             3            119 
[1] "STK32B MUTATION ANALYSIS"
[1] 3
  STK32B MUTATED STK32B WILD-TYPE 
               4              118 
  STK32B MUTATED STK32B WILD-TYPE 
               4              118 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 122 columns.

[1] "Batch" "21"   
[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=17,	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=87,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              19-3-2015 2-4-2015 25-9-2014
freq.values   "1"       "120"    "1"      
freq.contrast "121"     "2"      "121"    
both >= 3     "FALSE"   "FALSE"  "FALSE"  
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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)"
Variable 21:'BATCH_NUMBER':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
YEARS_TO_BIRTH, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 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
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  APC MUTATED   84 15
  APC WILD-TYPE 12  3
  APC MUTATED APC WILD-TYPE 
           99            15 
  APC MUTATED APC WILD-TYPE 
           15             3 
$`APC MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3580 
       14.50        16.83        15.39        20.02        10.39         8.02 
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-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
        2.01        50.04        12.03         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       37.02        36.03        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

$`APC WILD-TYPE`
TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       39.48        36.03        12.00        32.02        36.03         6.05 
TCGA-AG-3608 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 
       15.95        17.03        25.97        23.01        15.95         9.07 
TCGA-AG-A01L TCGA-DT-5265 TCGA-EI-6507 
       12.00         5.29        19.96 

  APC MUTATED APC WILD-TYPE 
         0.49          5.29 
  APC MUTATED APC WILD-TYPE 
       126.44         39.48 
  APC MUTATED APC WILD-TYPE 
        17.49         17.03 
[1] "0.5 - 126.4 (17.5)" "5.3 - 39.5 (17.0)" 
[1] "hr=" "1.9"
D1V2, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  APC MUTATED        26        4        23         2         5          4
  APC WILD-TYPE       1        3         6         0         0          0
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED           13          9       10         6
  APC WILD-TYPE          2          1        3         0
D1V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             26             1
  STAGE II             4             3
  STAGE IIA           23             6
  STAGE IIB            2             0
  STAGE III            5             0
  STAGE IIIA           4             0
  STAGE IIIB          13             2
  STAGE IIIC           9             1
  STAGE IV            10             3
  STAGE IVA            6             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 24 65  9
  APC WILD-TYPE  0  1 15  0
D1V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           8             0
  T2          24             1
  T3          65            15
  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   57 29 18
  APC WILD-TYPE 10  3  3
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          57            10
  N1          29             3
  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   79 14
  APC WILD-TYPE 13  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     79   14
  APC WILD-TYPE   13    3
   clus
vv  APC MUTATED APC WILD-TYPE
  0          79            13
  1          14             3
[1] 2 2
[1] FALSE
D1V7, binary
               cls
clus             0  1
  APC MUTATED   50 56
  APC WILD-TYPE  5 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     50   56
  APC WILD-TYPE    5   11
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          50             5
  MALE            56            11
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus             0  1
  APC MUTATED   93  7
  APC WILD-TYPE 13  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     93    7
  APC WILD-TYPE   13    3
                                clus
vv                               APC MUTATED APC WILD-TYPE
  RECTAL ADENOCARCINOMA                   93            13
  RECTAL MUCINOUS ADENOCARCINOMA           7             3
[1] 2 2
[1] FALSE
D1V9, binary
               cls
clus              0   1
  APC MUTATED     4 102
  APC WILD-TYPE   0  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      4  102
  APC WILD-TYPE    0   16
     clus
vv    APC MUTATED APC WILD-TYPE
  NO            4             0
  YES         102            16
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2 RX
  APC MUTATED   75  2  7  3
  APC WILD-TYPE 13  0  2  1
D1V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          75            13
  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
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED       0                         3    48
  APC WILD-TYPE     1                         0     2
D1V12, multiclass
                           clus
vv                          APC MUTATED APC WILD-TYPE
  ASIAN                               0             1
  BLACK OR AFRICAN AMERICAN           3             0
  WHITE                              48             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = CRIPAK MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED   10  1
  CRIPAK WILD-TYPE 86 17
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              11              103 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               1               17 
$`CRIPAK MUTATED`
TCGA-AF-2687 TCGA-AF-2693 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DD 
       24.13        19.10         6.05        12.99        13.97        57.24 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6465 TCGA-G5-6641 
       20.55        19.96        20.91        37.51        26.43 

$`CRIPAK WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 
        4.73        78.12         7.17        15.02        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6510 
       41.36        24.13        51.48        32.61         0.49        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 
       55.76 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            6.05             0.49 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           57.24           126.44 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           20.55            16.83 
[1] "6.0 - 57.2 (20.6)"  "0.5 - 126.4 (16.8)"
[1] "hr=" "1.8"
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         5          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRIPAK MUTATED            3          1        0         1
  CRIPAK WILD-TYPE         12          9       13         5
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                5
  STAGE IIIA              2                2
  STAGE IIIB              3               12
  STAGE IIIC              1                9
  STAGE IV                0               13
  STAGE IVA               1                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
  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 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
D2V9, binary
                  cls
clus                 0   1
  CRIPAK MUTATED     1  10
  CRIPAK WILD-TYPE   3 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      1   10
  CRIPAK WILD-TYPE    3  108
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO               1                3
  YES             10              108
[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
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRIPAK MUTATED       0                         1    10
  CRIPAK WILD-TYPE     1                         2    40
D2V12, multiclass
                           clus
vv                          CRIPAK MUTATED CRIPAK WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                 10               40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   73 11
  TP53 WILD-TYPE 23  7
  TP53 MUTATED TP53 WILD-TYPE 
            84             30 
  TP53 MUTATED TP53 WILD-TYPE 
            11              7 
$`TP53 MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       14.50        15.39        20.02        10.39        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-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         7.99         1.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       19.99        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W 
        6.02        23.01        37.02        15.95         9.07        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       64.01        10.98         1.94        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
      117.11         0.49        17.49         0.69         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        36.00        10.98        30.05        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        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 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 

$`TP53 WILD-TYPE`
TCGA-AF-2692 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       13.55        16.83        36.03         8.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 
       24.00         1.02        34.03        12.03         6.05         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
        0.99         1.02        36.95        13.02        14.01        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A025 TCGA-AG-A02G 
       13.94        25.97        36.03        12.00        49.97        38.96 
TCGA-AH-6547 TCGA-AH-6644 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-F5-6465 TCGA-G5-6641 
        1.45         0.72        12.95        32.61        37.51        26.43 

  TP53 MUTATED TP53 WILD-TYPE 
          0.49           0.72 
  TP53 MUTATED TP53 WILD-TYPE 
        126.44          49.97 
  TP53 MUTATED TP53 WILD-TYPE 
        17.885         15.420 
[1] "0.5 - 126.4 (17.9)" "0.7 - 50.0 (15.4)" 
[1] "hr=" "2.7"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TP53 MUTATED        17        6        22         2         3          2
  TP53 WILD-TYPE      10        1         7         0         2          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED           13          9        9         5
  TP53 WILD-TYPE          2          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             3              2
  STAGE IIIA            2              2
  STAGE IIIB           13              2
  STAGE IIIC            9              1
  STAGE IV              9              4
  STAGE IVA             5              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 61  9
  TP53 WILD-TYPE  5  8 19  0
D3V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            3              5
  T2           17              8
  T3           61             19
  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 25 16
  TP53 WILD-TYPE 19  7  5
D3V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           48             19
  N1           25              7
  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   68 12
  TP53 WILD-TYPE 24  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     68   12
  TP53 WILD-TYPE   24    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           68             24
  1           12              5
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus              0  1
  TP53 MUTATED   39 51
  TP53 WILD-TYPE 16 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     39   51
  TP53 WILD-TYPE   16   16
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           39             16
  MALE             51             16
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus              0  1
  TP53 MUTATED   83  5
  TP53 WILD-TYPE 23  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     83    5
  TP53 WILD-TYPE   23    5
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  RECTAL ADENOCARCINOMA                    83             23
  RECTAL MUCINOUS ADENOCARCINOMA            5              5
[1] 2 2
[1] FALSE
D3V9, binary
                cls
clus              0  1
  TP53 MUTATED    4 86
  TP53 WILD-TYPE  0 32
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   86
  TP53 WILD-TYPE    0   32
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             4              0
  YES           86             32
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   64  2  5  4
  TP53 WILD-TYPE 24  0  4  0
D3V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           64             24
  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
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       1                         3    42
  TP53 WILD-TYPE     0                         0     8
D3V12, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                1              0
  BLACK OR AFRICAN AMERICAN            3              0
  WHITE                               42              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MUC4 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  MUC4 MUTATED   20  4
  MUC4 WILD-TYPE 76 14
  MUC4 MUTATED MUC4 WILD-TYPE 
            24             90 
  MUC4 MUTATED MUC4 WILD-TYPE 
             4             14 
$`MUC4 MUTATED`
TCGA-AF-2687 TCGA-AF-2693 TCGA-AG-3731 TCGA-AG-A002 TCGA-AH-6544 TCGA-AH-6547 
       24.13        19.10         1.02        20.98         0.49         1.45 
TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 
        6.05         6.05        12.99        13.97        10.98        13.05 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
      126.44        57.24        24.13         0.49        19.96        20.91 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       37.51        31.30        28.57         0.69        55.76        26.43 

$`MUC4 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        0.99        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04       117.11        17.49         0.69         0.72 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6157 
        6.97         4.73        78.12         7.17        15.02        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DG 
       30.05        12.95        10.06         5.29        41.36        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6812 
       32.61        20.55        18.28         9.96        32.19         0.66 

  MUC4 MUTATED MUC4 WILD-TYPE 
          0.49           0.66 
  MUC4 MUTATED MUC4 WILD-TYPE 
        126.44         117.11 
  MUC4 MUTATED MUC4 WILD-TYPE 
         19.53          17.03 
[1] "0.5 - 126.4 (19.5)" "0.7 - 117.1 (17.0)"
[1] "hr=" "1.1"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  MUC4 MUTATED         3        0         5         1         1          2
  MUC4 WILD-TYPE      24        7        24         1         4          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC4 MUTATED            4          3        2         2
  MUC4 WILD-TYPE         11          7       11         4
D4V3, multiclass
            clus
vv           MUC4 MUTATED MUC4 WILD-TYPE
  STAGE I               3             24
  STAGE II              0              7
  STAGE IIA             5             24
  STAGE IIB             1              1
  STAGE III             1              4
  STAGE IIIA            2              2
  STAGE IIIB            4             11
  STAGE IIIC            3              7
  STAGE IV              2             11
  STAGE IVA             2              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
  MUC4 MUTATED    1  4 18  2
  MUC4 WILD-TYPE  7 21 62  7
D4V4, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  T1            1              7
  T2            4             21
  T3           18             62
  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
  MUC4 MUTATED   10 12  3
  MUC4 WILD-TYPE 57 20 18
D4V5, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  N0           10             57
  N1           12             20
  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"
D4V6, binary
                cls
clus              0  1
  MUC4 MUTATED   15  5
  MUC4 WILD-TYPE 77 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     15    5
  MUC4 WILD-TYPE   77   12
   clus
vv  MUC4 MUTATED MUC4 WILD-TYPE
  0           15             77
  1            5             12
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus              0  1
  MUC4 MUTATED   10 15
  MUC4 WILD-TYPE 45 52
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     10   15
  MUC4 WILD-TYPE   45   52
        clus
vv       MUC4 MUTATED MUC4 WILD-TYPE
  FEMALE           10             45
  MALE             15             52
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus              0  1
  MUC4 MUTATED   23  1
  MUC4 WILD-TYPE 83  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     23    1
  MUC4 WILD-TYPE   83    9
                                clus
vv                               MUC4 MUTATED MUC4 WILD-TYPE
  RECTAL ADENOCARCINOMA                    23             83
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 2 2
[1] FALSE
D4V9, binary
                cls
clus              0  1
  MUC4 MUTATED    1 24
  MUC4 WILD-TYPE  3 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED      1   24
  MUC4 WILD-TYPE    3   94
     clus
vv    MUC4 MUTATED MUC4 WILD-TYPE
  NO             1              3
  YES           24             94
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  MUC4 MUTATED   14  1  1  0
  MUC4 WILD-TYPE 74  1  8  4
D4V10, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  R0           14             74
  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"
D4V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC4 MUTATED       0                         1    22
  MUC4 WILD-TYPE     1                         2    28
D4V12, multiclass
                           clus
vv                          MUC4 MUTATED MUC4 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                               22             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = TCF7L2 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  TCF7L2 MUTATED   11  2
  TCF7L2 WILD-TYPE 85 16
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              13              101 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               2               16 
$`TCF7L2 MUTATED`
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3726 TCGA-AG-3882 
       13.55        14.50        20.02        36.03         7.99        19.99 
TCGA-AG-3898 TCGA-AG-4007 TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-DC-6683 
       48.03         1.02        38.04         0.49         6.05        10.06 
TCGA-DY-A1DG 
       51.48 

$`TCF7L2 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        19.10        12.72        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        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-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99        19.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       38.96        61.97        41.00       117.11         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        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        37.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.49             0.49 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           51.48           126.44 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           14.50            17.49 
[1] "0.5 - 51.5 (14.5)"  "0.5 - 126.4 (17.5)"
[1] "hr=" "1.1"
D5V2, 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         5          3
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7L2 MUTATED            2          0        3         2
  TCF7L2 WILD-TYPE         13         10       10         4
D5V3, 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                5
  STAGE IIIA              1                3
  STAGE IIIB              2               13
  STAGE IIIC              0               10
  STAGE IV                3               10
  STAGE IVA               2                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
  TCF7L2 MUTATED    0  3  8  2
  TCF7L2 WILD-TYPE  8 22 72  7
D5V4, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                8
  T2              3               22
  T3              8               72
  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
  TCF7L2 MUTATED    4  7  2
  TCF7L2 WILD-TYPE 63 25 19
D5V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0              4               63
  N1              7               25
  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"
D5V6, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    7  5
  TCF7L2 WILD-TYPE 85 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      7    5
  TCF7L2 WILD-TYPE   85   12
   clus
vv  TCF7L2 MUTATED TCF7L2 WILD-TYPE
  0              7               85
  1              5               12
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    3 10
  TCF7L2 WILD-TYPE 52 57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      3   10
  TCF7L2 WILD-TYPE   52   57
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE              3               52
  MALE               10               57
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus                0  1
  TCF7L2 MUTATED   11  0
  TCF7L2 WILD-TYPE 95 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     11    0
  TCF7L2 WILD-TYPE   95   10
                                clus
vv                               TCF7L2 MUTATED TCF7L2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      11               95
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
D5V9, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED     0  13
  TCF7L2 WILD-TYPE   4 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      0   13
  TCF7L2 WILD-TYPE    4  105
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  NO               0                4
  YES             13              105
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  TCF7L2 MUTATED    8  0  2  0
  TCF7L2 WILD-TYPE 80  2  7  4
D5V10, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0              8               80
  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"
D5V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCF7L2 MUTATED       0                         0     7
  TCF7L2 WILD-TYPE     1                         3    43
D5V12, multiclass
                           clus
vv                          TCF7L2 MUTATED TCF7L2 WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  7               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = FMN2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  FMN2 MUTATED   10  3
  FMN2 WILD-TYPE 86 15
  FMN2 MUTATED FMN2 WILD-TYPE 
            13            101 
  FMN2 MUTATED FMN2 WILD-TYPE 
             3             15 
$`FMN2 MUTATED`
TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-A026 TCGA-AH-6547 TCGA-CI-6619 TCGA-CI-6622 
       32.98        19.99         1.94         1.45         6.05         6.97 
TCGA-CL-5917 TCGA-DC-5869 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       78.12        12.99        13.05         5.29       126.44        41.36 
TCGA-DY-A1DG 
       51.48 

$`FMN2 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        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         0.49        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 
        0.69         0.72         6.05         4.73         7.17        15.02 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        36.00        10.98        30.05        12.95        10.06 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        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        37.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FMN2 MUTATED FMN2 WILD-TYPE 
          1.45           0.49 
  FMN2 MUTATED FMN2 WILD-TYPE 
        126.44         117.11 
  FMN2 MUTATED FMN2 WILD-TYPE 
         13.05          17.49 
[1] "1.4 - 126.4 (13.1)" "0.5 - 117.1 (17.5)"
[1] "hr=" "1"  
D6V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMN2 MUTATED            1          1        1         1
  FMN2 WILD-TYPE         14          9       12         5
D6V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            1             14
  STAGE IIIC            1              9
  STAGE IV              1             12
  STAGE IVA             1              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
  FMN2 MUTATED    0  2 10  2
  FMN2 WILD-TYPE  8 23 70  7
D6V4, 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
D6V5, 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"
D6V6, 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
D6V7, 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
D6V8, 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
D6V9, binary
                cls
clus               0   1
  FMN2 MUTATED     0  14
  FMN2 WILD-TYPE   4 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED      0   14
  FMN2 WILD-TYPE    4  104
     clus
vv    FMN2 MUTATED FMN2 WILD-TYPE
  NO             0              4
  YES           14            104
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  FMN2 MUTATED    4  1  0  2
  FMN2 WILD-TYPE 84  1  9  2
D6V10, 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"
D6V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FMN2 MUTATED       1                         1     8
  FMN2 WILD-TYPE     0                         2    42
D6V12, multiclass
                           clus
vv                          FMN2 MUTATED FMN2 WILD-TYPE
  ASIAN                                1              0
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                8             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = SHROOM4 MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  SHROOM4 MUTATED    6  1
  SHROOM4 WILD-TYPE 90 17
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                7               107 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                1                17 
$`SHROOM4 MUTATED`
TCGA-AF-5654 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 
       16.83         7.17        12.99        13.97        30.05        20.55 
TCGA-F5-6813 
        0.69 

$`SHROOM4 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6157 
        6.05         6.97         4.73        78.12        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        12.95        13.05        10.06         5.29       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         0.49 
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        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             0.69              0.49 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            30.05            126.44 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            13.97             18.28 
[1] "0.7 - 30.1 (14.0)"  "0.5 - 126.4 (18.3)"
[1] "hr=" "2.3"
D7V2, 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         5          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SHROOM4 MUTATED            1          1        0         0
  SHROOM4 WILD-TYPE         14          9       13         6
D7V3, 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                 5
  STAGE IIIA               1                 3
  STAGE IIIB               1                14
  STAGE IIIC               1                 9
  STAGE IV                 0                13
  STAGE IVA                0                 6
[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
D7V4, 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
D7V5, 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"
D7V6, 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
D7V7, 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
D7V8, 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
D7V9, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     0   7
  SHROOM4 WILD-TYPE   4 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      0    7
  SHROOM4 WILD-TYPE    4  111
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                0                 4
  YES               7               111
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  SHROOM4 MUTATED    6  0  0  1
  SHROOM4 WILD-TYPE 82  2  9  3
D7V10, 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"
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED       0                         1     6
  SHROOM4 WILD-TYPE     1                         2    44
D7V12, multiclass
                           clus
vv                          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                   6                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = RPTN MUTATION ANALYSIS
D8V1, survival
                sevent
clus2             0  1
  RPTN MUTATED    3  2
  RPTN WILD-TYPE 93 16
  RPTN MUTATED RPTN WILD-TYPE 
             5            109 
  RPTN MUTATED RPTN WILD-TYPE 
             2             16 
$`RPTN MUTATED`
TCGA-AG-3732 TCGA-AH-6549 TCGA-DC-5869 TCGA-DY-A1DF TCGA-F5-6464 
       32.98        17.49        12.99        24.13         9.96 

$`RPTN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        0.49         1.45         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RPTN MUTATED RPTN WILD-TYPE 
          9.96           0.49 
  RPTN MUTATED RPTN WILD-TYPE 
         32.98         126.44 
  RPTN MUTATED RPTN WILD-TYPE 
         17.49          17.03 
[1] "10.0 - 33.0 (17.5)" "0.5 - 126.4 (17.0)"
[1] "hr=" "4.6"
D8V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPTN MUTATED            1          2        0         0
  RPTN WILD-TYPE         14          8       13         6
D8V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            1             14
  STAGE IIIC            2              8
  STAGE IV              0             13
  STAGE IVA             0              6
[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
D8V4, 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
D8V5, 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"
D8V6, 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
D8V7, 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
D8V8, 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
D8V9, binary
                cls
clus               0   1
  RPTN MUTATED     0   5
  RPTN WILD-TYPE   4 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0    5
  RPTN WILD-TYPE    4  113
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO             0              4
  YES            5            113
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  RPTN MUTATED    3  0  0  1
  RPTN WILD-TYPE 85  2  9  3
D8V10, 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"
D8V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         1     3
  RPTN WILD-TYPE     1                         2    47
D8V12, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = NRAS MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  NRAS MUTATED   10  1
  NRAS WILD-TYPE 86 17
  NRAS MUTATED NRAS WILD-TYPE 
            11            103 
  NRAS MUTATED NRAS WILD-TYPE 
             1             17 
$`NRAS MUTATED`
TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A01L 
       43.04        10.39        15.39        13.02        14.01        12.00 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6682 TCGA-EI-6510 TCGA-F5-6465 
       15.02        30.05        13.05        18.28        37.51 

$`NRAS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       24.13        39.48        13.55        19.10        12.72        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03         9.07        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11         0.49         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 
       12.99        13.97        36.00        10.98        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       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-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NRAS MUTATED NRAS WILD-TYPE 
         10.39           0.49 
  NRAS MUTATED NRAS WILD-TYPE 
         43.04         126.44 
  NRAS MUTATED NRAS WILD-TYPE 
         15.02          19.10 
[1] "10.4 - 43.0 (15.0)" "0.5 - 126.4 (19.1)"
[1] "hr=" "1.4"
D9V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED            2          0        1         1
  NRAS WILD-TYPE         13         10       12         5
D9V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            2             13
  STAGE IIIC            0             10
  STAGE IV              1             12
  STAGE IVA             1              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
D9V4, 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
D9V5, 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"
D9V6, 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
D9V7, 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
D9V8, 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
D9V9, binary
                cls
clus               0   1
  NRAS MUTATED     1  10
  NRAS WILD-TYPE   3 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1   10
  NRAS WILD-TYPE    3  108
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             1              3
  YES           10            108
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  NRAS MUTATED   10  0  0  0
  NRAS WILD-TYPE 78  2  9  4
D9V10, 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"
D9V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         1     7
  NRAS WILD-TYPE     1                         2    43
D9V12, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                7             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = CDH1 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  CDH1 MUTATED   11  1
  CDH1 WILD-TYPE 85 17
  CDH1 MUTATED CDH1 WILD-TYPE 
            12            102 
  CDH1 MUTATED CDH1 WILD-TYPE 
             1             17 
$`CDH1 MUTATED`
TCGA-AF-2687 TCGA-AF-6136 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3892 TCGA-AH-6544 
       24.13        15.39         1.02        32.98        13.02         0.49 
TCGA-AH-6643 TCGA-DC-5337 TCGA-DY-A1DG TCGA-EF-5830 TCGA-F5-6465 TCGA-G5-6235 
        0.69        15.02        51.48         0.49        37.51        55.76 

$`CDH1 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
       38.04       117.11         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
        6.05         6.97         4.73        78.12         7.17        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        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 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.49           0.66 
  CDH1 MUTATED CDH1 WILD-TYPE 
         55.76         126.44 
  CDH1 MUTATED CDH1 WILD-TYPE 
        15.205         17.885 
[1] "0.5 - 55.8 (15.2)"  "0.7 - 126.4 (17.9)"
[1] "hr=" "2.1"
D10V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH1 MUTATED            2          2        1         1
  CDH1 WILD-TYPE         13          8       12         5
D10V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            2             13
  STAGE IIIC            2              8
  STAGE IV              1             12
  STAGE IVA             1              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
  CDH1 MUTATED    2  1  8  1
  CDH1 WILD-TYPE  6 24 72  8
D10V4, 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
D10V5, 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"
D10V6, 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
D10V7, 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
D10V8, 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
D10V9, binary
                cls
clus               0   1
  CDH1 MUTATED     2  10
  CDH1 WILD-TYPE   2 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      2   10
  CDH1 WILD-TYPE    2  108
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO             2              2
  YES           10            108
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  CDH1 MUTATED    7  1  1  0
  CDH1 WILD-TYPE 81  1  8  4
D10V10, 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"
D10V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED       0                         0     9
  CDH1 WILD-TYPE     1                         3    41
D10V12, multiclass
                           clus
vv                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                9             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = ARID1A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    8  3
  ARID1A WILD-TYPE 88 15
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              103 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               15 
$`ARID1A MUTATED`
TCGA-AF-2687 TCGA-AF-2693 TCGA-AG-3574 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A00H 
       24.13        19.10        36.03         0.99        13.02        25.97 
TCGA-AG-A025 TCGA-CI-6620 TCGA-CI-6624 TCGA-DY-A1DF TCGA-DY-A1DG 
       49.97         6.05         4.73        24.13        51.48 

$`ARID1A WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        41.36        57.24        32.61         0.49 
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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.49 
  ARID1A MUTATED ARID1A WILD-TYPE 
           51.48           126.44 
  ARID1A MUTATED ARID1A WILD-TYPE 
           24.13            17.03 
[1] "1.0 - 51.5 (24.1)"  "0.5 - 126.4 (17.0)"
[1] "hr=" "1.7"
D11V2, 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         5          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID1A MUTATED            0          2        0         2
  ARID1A WILD-TYPE         15          8       13         4
D11V3, 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                5
  STAGE IIIA              0                4
  STAGE IIIB              0               15
  STAGE IIIC              2                8
  STAGE IV                0               13
  STAGE IVA               2                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
  ARID1A MUTATED    2  3  6  0
  ARID1A WILD-TYPE  6 22 74  9
D11V4, 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
D11V5, 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"
D11V6, 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
D11V7, 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
D11V8, 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
D11V9, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  10
  ARID1A WILD-TYPE   3 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   10
  ARID1A WILD-TYPE    3  108
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               1                3
  YES             10              108
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  ARID1A MUTATED    6  0  0  0
  ARID1A WILD-TYPE 82  2  9  4
D11V10, 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"
D11V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0     6
  ARID1A WILD-TYPE     1                         3    44
D11V12, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  6               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = RBM38 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  RBM38 MUTATED    7  0
  RBM38 WILD-TYPE 89 18
  RBM38 MUTATED RBM38 WILD-TYPE 
              7             107 
  RBM38 MUTATED RBM38 WILD-TYPE 
              0              18 
$`RBM38 MUTATED`
TCGA-AF-2687 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-F5-6571 TCGA-F5-6811 
       24.13         0.69         6.05         6.05        31.30        32.19 
TCGA-F5-6813 
        0.69 

$`RBM38 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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-6644 TCGA-CI-6622 TCGA-CI-6624 
        0.49         1.45        17.49         0.72         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
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 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       37.51        28.57         0.66        55.76        26.43 

  RBM38 MUTATED RBM38 WILD-TYPE 
           0.69            0.49 
  RBM38 MUTATED RBM38 WILD-TYPE 
          32.19          126.44 
  RBM38 MUTATED RBM38 WILD-TYPE 
           6.05           17.49 
[1] "0.7 - 32.2 (6.0)"   "0.5 - 126.4 (17.5)"
[1] "hr="     "2.6e+07"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RBM38 MUTATED         0        0         2         0         1          0
  RBM38 WILD-TYPE      27        7        27         2         4          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM38 MUTATED            0          3        1         1
  RBM38 WILD-TYPE         15          7       12         5
D12V3, multiclass
            clus
vv           RBM38 MUTATED RBM38 WILD-TYPE
  STAGE I                0              27
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              1               4
  STAGE IIIA             0               4
  STAGE IIIB             0              15
  STAGE IIIC             3               7
  STAGE IV               1              12
  STAGE IVA              1               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
  RBM38 MUTATED    0  0  7  1
  RBM38 WILD-TYPE  8 25 73  8
D12V4, multiclass
    clus
vv   RBM38 MUTATED RBM38 WILD-TYPE
  T1             0               8
  T2             0              25
  T3             7              73
  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
  RBM38 MUTATED    2  3  3
  RBM38 WILD-TYPE 65 29 18
D12V5, multiclass
    clus
vv   RBM38 MUTATED RBM38 WILD-TYPE
  N0             2              65
  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
  RBM38 MUTATED    5  2
  RBM38 WILD-TYPE 87 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED      5    2
  RBM38 WILD-TYPE   87   15
   clus
vv  RBM38 MUTATED RBM38 WILD-TYPE
  0             5              87
  1             2              15
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus               0  1
  RBM38 MUTATED    3  5
  RBM38 WILD-TYPE 52 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED      3    5
  RBM38 WILD-TYPE   52   62
        clus
vv       RBM38 MUTATED RBM38 WILD-TYPE
  FEMALE             3              52
  MALE               5              62
[1] 2 2
[1] FALSE
D12V8, binary
                 cls
clus               0  1
  RBM38 MUTATED    8  0
  RBM38 WILD-TYPE 98 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED      8    0
  RBM38 WILD-TYPE   98   10
                                clus
vv                               RBM38 MUTATED RBM38 WILD-TYPE
  RECTAL ADENOCARCINOMA                      8              98
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
D12V9, binary
                 cls
clus                0   1
  RBM38 MUTATED     1   7
  RBM38 WILD-TYPE   3 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED      1    7
  RBM38 WILD-TYPE    3  111
     clus
vv    RBM38 MUTATED RBM38 WILD-TYPE
  NO              1               3
  YES             7             111
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  RBM38 MUTATED    4  0  0  0
  RBM38 WILD-TYPE 84  2  9  4
D12V10, multiclass
    clus
vv   RBM38 MUTATED RBM38 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"
D12V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM38 MUTATED       0                         0     8
  RBM38 WILD-TYPE     1                         3    42
D12V12, multiclass
                           clus
vv                          RBM38 MUTATED RBM38 WILD-TYPE
  ASIAN                                 0               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 8              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = SMAD2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  SMAD2 MUTATED    7  0
  SMAD2 WILD-TYPE 89 18
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              7             107 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              0              18 
$`SMAD2 MUTATED`
TCGA-AG-3608 TCGA-AG-3890 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A01W TCGA-F5-6465 
       15.95        17.03        20.98        37.02        70.03        37.51 
TCGA-G5-6235 
       55.76 

$`SMAD2 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3609 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       23.01        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11         0.49         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       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         0.49 
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        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
          15.95            0.49 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          70.03          126.44 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          37.02           16.83 
[1] "15.9 - 70.0 (37.0)" "0.5 - 126.4 (16.8)"
[1] "hr="     "8.2e+07"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD2 MUTATED         2        1         3         0         0          0
  SMAD2 WILD-TYPE      25        6        26         2         5          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED            1          0        0         0
  SMAD2 WILD-TYPE         14         10       13         6
D13V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                2              25
  STAGE II               1               6
  STAGE IIA              3              26
  STAGE IIB              0               2
  STAGE III              0               5
  STAGE IIIA             0               4
  STAGE IIIB             1              14
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               6
[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  5  0
  SMAD2 WILD-TYPE  8 23 75  9
D13V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               8
  T2             2              23
  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
  SMAD2 MUTATED    6  1  0
  SMAD2 WILD-TYPE 61 31 21
D13V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             6              61
  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"
D13V6, binary
                 cls
clus               0  1
  SMAD2 MUTATED    6  0
  SMAD2 WILD-TYPE 86 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      6    0
  SMAD2 WILD-TYPE   86   17
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0             6              86
  1             0              17
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus               0  1
  SMAD2 MUTATED    3  4
  SMAD2 WILD-TYPE 52 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      3    4
  SMAD2 WILD-TYPE   52   63
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             3              52
  MALE               4              63
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus               0  1
  SMAD2 MUTATED    7  0
  SMAD2 WILD-TYPE 99 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      7    0
  SMAD2 WILD-TYPE   99   10
                                clus
vv                               SMAD2 MUTATED SMAD2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
D13V9, binary
                 cls
clus                0   1
  SMAD2 MUTATED     0   7
  SMAD2 WILD-TYPE   4 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      0    7
  SMAD2 WILD-TYPE    4  111
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO              0               4
  YES             7             111
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  SMAD2 MUTATED    6  1  0  0
  SMAD2 WILD-TYPE 82  1  9  4
D13V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             6              82
  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"
D13V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD2 MUTATED       0                         0     2
  SMAD2 WILD-TYPE     1                         3    48
D13V12, multiclass
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2              52 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6571      TCGA-F5-6702 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6641 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 

Clustering(14) Variable = VCX2 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  VCX2 MUTATED    3  2
  VCX2 WILD-TYPE 93 16
  VCX2 MUTATED VCX2 WILD-TYPE 
             5            109 
  VCX2 MUTATED VCX2 WILD-TYPE 
             2             16 
$`VCX2 MUTATED`
TCGA-AH-6547 TCGA-CI-6619 TCGA-CL-5918 TCGA-DY-A1DD TCGA-F5-6702 
        1.45         6.05         7.17        57.24        28.57 

$`VCX2 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-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-6620 
      117.11         0.49        17.49         0.69         0.72         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       37.51        31.30        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VCX2 MUTATED VCX2 WILD-TYPE 
          1.45           0.49 
  VCX2 MUTATED VCX2 WILD-TYPE 
         57.24         126.44 
  VCX2 MUTATED VCX2 WILD-TYPE 
          7.17          17.49 
[1] "1.4 - 57.2 (7.2)"   "0.5 - 126.4 (17.5)"
[1] "hr=" "2.4"
D14V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCX2 MUTATED            1          0        1         1
  VCX2 WILD-TYPE         14         10       12         5
D14V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            1             14
  STAGE IIIC            0             10
  STAGE IV              1             12
  STAGE IVA             1              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
  VCX2 MUTATED    0  0  5  0
  VCX2 WILD-TYPE  8 25 75  9
D14V4, 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
D14V5, 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"
D14V6, 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
D14V7, 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
D14V8, 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
D14V9, binary
                cls
clus               0   1
  VCX2 MUTATED     0   5
  VCX2 WILD-TYPE   4 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      0    5
  VCX2 WILD-TYPE    4  113
     clus
vv    VCX2 MUTATED VCX2 WILD-TYPE
  NO             0              4
  YES            5            113
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  VCX2 MUTATED    1  0  0  1
  VCX2 WILD-TYPE 87  2  9  3
D14V10, multiclass
[1] "Remove cluster labels:" "VCX2 MUTATED"          
clus
  VCX2 MUTATED VCX2 WILD-TYPE 
             2            101 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-DC-5337 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6812     TCGA-F5-6813     TCGA-G5-6235 
"VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" "VCX2 WILD-TYPE" 
    TCGA-G5-6641 
"VCX2 WILD-TYPE" 
D14V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VCX2 MUTATED       0                         0     5
  VCX2 WILD-TYPE     1                         3    45
D14V12, multiclass
                           clus
vv                          VCX2 MUTATED VCX2 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                5             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = ERBB2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  ERBB2 MUTATED    7  1
  ERBB2 WILD-TYPE 89 17
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             106 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              1              17 
$`ERBB2 MUTATED`
TCGA-AF-2693 TCGA-AG-3599 TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-3902 TCGA-AH-6544 
       19.10        12.03        32.98        48.03        32.02         0.49 
TCGA-AH-6644 TCGA-F5-6464 
        0.72         9.96 

$`ERBB2 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        0.99         1.02         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
       38.04       117.11         1.45        17.49         0.69         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       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         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        37.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           0.49            0.49 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          48.03          126.44 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         15.565          17.260 
[1] "0.5 - 48.0 (15.6)"  "0.5 - 126.4 (17.3)"
[1] "hr=" "1"  
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ERBB2 MUTATED         3        0         2         0         0          0
  ERBB2 WILD-TYPE      24        7        27         2         5          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED            0          1        0         0
  ERBB2 WILD-TYPE         15          9       13         6
D15V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                3              24
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              0               2
  STAGE III              0               5
  STAGE IIIA             0               4
  STAGE IIIB             0              15
  STAGE IIIC             1               9
  STAGE IV               0              13
  STAGE IVA              0               6
[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  3  4  1
  ERBB2 WILD-TYPE  8 22 76  8
D15V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 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
  ERBB2 MUTATED    5  1  1
  ERBB2 WILD-TYPE 62 31 20
D15V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             5              62
  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
  ERBB2 MUTATED    5  1
  ERBB2 WILD-TYPE 87 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      5    1
  ERBB2 WILD-TYPE   87   16
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0             5              87
  1             1              16
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  ERBB2 MUTATED    2  6
  ERBB2 WILD-TYPE 53 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      2    6
  ERBB2 WILD-TYPE   53   61
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             2              53
  MALE               6              61
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED     6   0
  ERBB2 WILD-TYPE 100  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      6    0
  ERBB2 WILD-TYPE  100   10
                                clus
vv                               ERBB2 MUTATED ERBB2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
D15V9, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0   8
  ERBB2 WILD-TYPE   4 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    8
  ERBB2 WILD-TYPE    4  110
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              0               4
  YES             8             110
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  ERBB2 MUTATED    5  0  0  0
  ERBB2 WILD-TYPE 83  2  9  4
D15V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 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"
D15V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       0                         0     4
  ERBB2 WILD-TYPE     1                         3    46
D15V12, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 0               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = RBM10 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2              0  1
  RBM10 MUTATED    3  2
  RBM10 WILD-TYPE 93 16
  RBM10 MUTATED RBM10 WILD-TYPE 
              5             109 
  RBM10 MUTATED RBM10 WILD-TYPE 
              2              16 
$`RBM10 MUTATED`
TCGA-AF-2689 TCGA-AG-3583 TCGA-AG-3902 TCGA-AG-3999 TCGA-EI-6510 
       39.48        20.05        32.02        28.04        18.28 

$`RBM10 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
        1.02        48.03        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11         0.49         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
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-F5-6465 
        0.49        20.55        19.96        20.91         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RBM10 MUTATED RBM10 WILD-TYPE 
          18.28            0.49 
  RBM10 MUTATED RBM10 WILD-TYPE 
          39.48          126.44 
  RBM10 MUTATED RBM10 WILD-TYPE 
          28.04           16.83 
[1] "18.3 - 39.5 (28.0)" "0.5 - 126.4 (16.8)"
[1] "hr=" "2.5"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RBM10 MUTATED         0        0         1         0         0          0
  RBM10 WILD-TYPE      27        7        28         2         5          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM10 MUTATED            0          1        2         1
  RBM10 WILD-TYPE         15          9       11         5
D16V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0              27
  STAGE II               0               7
  STAGE IIA              1              28
  STAGE IIB              0               2
  STAGE III              0               5
  STAGE IIIA             0               4
  STAGE IIIB             0              15
  STAGE IIIC             1               9
  STAGE IV               2              11
  STAGE IVA              1               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  1  4  0
  RBM10 WILD-TYPE  8 24 76  9
D16V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             0               8
  T2             1              24
  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    2  0  3
  RBM10 WILD-TYPE 65 32 18
D16V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0             2              65
  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"
D16V6, binary
                 cls
clus               0  1
  RBM10 MUTATED    2  2
  RBM10 WILD-TYPE 90 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE   90   15
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             2              90
  1             2              15
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  2
  RBM10 WILD-TYPE 52 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    2
  RBM10 WILD-TYPE   52   65
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             3              52
  MALE               2              65
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  RBM10 MUTATED     4   1
  RBM10 WILD-TYPE 102   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4    1
  RBM10 WILD-TYPE  102    9
                                clus
vv                               RBM10 MUTATED RBM10 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 2 2
[1] FALSE
D16V9, binary
                 cls
clus                0   1
  RBM10 MUTATED     0   5
  RBM10 WILD-TYPE   4 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0    5
  RBM10 WILD-TYPE    4  113
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              0               4
  YES             5             113
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  RBM10 MUTATED    4  0  1  0
  RBM10 WILD-TYPE 84  2  8  4
D16V10, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             4              84
  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"
D16V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       0                         0     2
  RBM10 WILD-TYPE     1                         3    48
D16V12, multiclass
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              2              52 
     TCGA-AF-2687      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-2693 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672      TCGA-AH-6544 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643      TCGA-AH-6644 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621      TCGA-CI-6622 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918      TCGA-DC-5337 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EF-5830 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508      TCGA-F5-6464 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 

Clustering(17) Variable = PON3 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  PON3 MUTATED    3  1
  PON3 WILD-TYPE 93 17
  PON3 MUTATED PON3 WILD-TYPE 
             4            110 
  PON3 MUTATED PON3 WILD-TYPE 
             1             17 
$`PON3 MUTATED`
TCGA-AF-2693 TCGA-CI-6620 TCGA-CL-5918 TCGA-DY-A1DG 
       19.10         6.05         7.17        51.48 

$`PON3 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        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 
       37.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PON3 MUTATED PON3 WILD-TYPE 
          6.05           0.49 
  PON3 MUTATED PON3 WILD-TYPE 
         51.48         126.44 
  PON3 MUTATED PON3 WILD-TYPE 
        13.135         17.260 
[1] "6.0 - 51.5 (13.1)"  "0.5 - 126.4 (17.3)"
[1] "hr=" "1.5"
D17V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PON3 MUTATED            0          0        0         2
  PON3 WILD-TYPE         15         10       13         4
D17V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            0             15
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             2              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
  PON3 MUTATED    0  1  3  0
  PON3 WILD-TYPE  8 24 77  9
D17V4, 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
D17V5, 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"
D17V6, 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
D17V7, 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
D17V8, 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
D17V9, binary
                cls
clus               0   1
  PON3 MUTATED     0   4
  PON3 WILD-TYPE   4 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      0    4
  PON3 WILD-TYPE    4  114
     clus
vv    PON3 MUTATED PON3 WILD-TYPE
  NO             0              4
  YES            4            114
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  PON3 MUTATED    0  0  0  1
  PON3 WILD-TYPE 88  2  9  3
D17V10, multiclass
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             1            102 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     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-A00H 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     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-DT-5265     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812     TCGA-F5-6813 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" 
D17V11, continuous
[1] "Remove cluster labels:" "PON3 MUTATED"          
clus
  PON3 MUTATED PON3 WILD-TYPE 
             2            111 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AG-3574 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3611 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3881 
"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-3890     TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6544 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6622 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-DY-A1DF     TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"PON3 WILD-TYPE" "PON3 WILD-TYPE" "PON3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PON3 MUTATED       0                         0     4
  PON3 WILD-TYPE     1                         3    46
D17V12, multiclass
                           clus
vv                          PON3 MUTATED PON3 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                4             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = HIST2H2AC MUTATION ANALYSIS
D18V1, survival
                     sevent
clus2                  0  1
  HIST2H2AC MUTATED    3  0
  HIST2H2AC WILD-TYPE 93 18
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  3                 111 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  0                  18 
$`HIST2H2AC MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-F5-6812 
       24.13        14.50         0.66 

$`HIST2H2AC WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        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        37.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
               0.66                0.49 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
              24.13              126.44 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
              14.50               17.49 
[1] "0.7 - 24.1 (14.5)"  "0.5 - 126.4 (17.5)"
[1] "hr="     "9200000"
D18V2, continuous
                     vv
clus                  STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  HIST2H2AC MUTATED         0        0         1         0         0          0
  HIST2H2AC WILD-TYPE      27        7        28         2         5          4
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIST2H2AC MUTATED            0          1        0         1
  HIST2H2AC WILD-TYPE         15          9       13         5
D18V3, multiclass
            clus
vv           HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  STAGE I                    0                  27
  STAGE II                   0                   7
  STAGE IIA                  1                  28
  STAGE IIB                  0                   2
  STAGE III                  0                   5
  STAGE IIIA                 0                   4
  STAGE IIIB                 0                  15
  STAGE IIIC                 1                   9
  STAGE IV                   0                  13
  STAGE IVA                  1                   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
  HIST2H2AC MUTATED    0  0  2  1
  HIST2H2AC WILD-TYPE  8 25 78  8
D18V4, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  T1                 0                   8
  T2                 0                  25
  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
  HIST2H2AC MUTATED    1  0  2
  HIST2H2AC WILD-TYPE 66 32 19
D18V5, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC 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"
D18V6, binary
                     cls
clus                   0  1
  HIST2H2AC MUTATED    2  0
  HIST2H2AC WILD-TYPE 90 17
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      2    0
  HIST2H2AC WILD-TYPE   90   17
   clus
vv  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  0                 2                  90
  1                 0                  17
[1] 2 2
[1] FALSE
D18V7, binary
                     cls
clus                   0  1
  HIST2H2AC MUTATED    0  3
  HIST2H2AC WILD-TYPE 55 64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      0    3
  HIST2H2AC WILD-TYPE   55   64
        clus
vv       HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  FEMALE                 0                  55
  MALE                   3                  64
[1] 2 2
[1] FALSE
D18V8, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     2   0
  HIST2H2AC WILD-TYPE 104  10
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      2    0
  HIST2H2AC WILD-TYPE  104   10
                                clus
vv                               HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 2 2
[1] FALSE
D18V9, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     1   2
  HIST2H2AC WILD-TYPE   3 116
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      1    2
  HIST2H2AC WILD-TYPE    3  116
     clus
vv    HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  NO                  1                   3
  YES                 2                 116
[1] 2 2
[1] FALSE
                     vv
clus                  R0 R1 R2 RX
  HIST2H2AC MUTATED    3  0  0  0
  HIST2H2AC WILD-TYPE 85  2  9  4
D18V10, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC 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"
D18V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST2H2AC MUTATED       0                         0     3
  HIST2H2AC WILD-TYPE     1                         3    47
D18V12, multiclass
                           clus
vv                          HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  ASIAN                                     0                   1
  BLACK OR AFRICAN AMERICAN                 0                   3
  WHITE                                     3                  47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = CTNNB1 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED   16  2
  CTNNB1 WILD-TYPE 80 16
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              18               96 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               2               16 
$`CTNNB1 MUTATED`
TCGA-AF-2693 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A020 
       19.10        20.02        12.00        32.98        13.02        10.98 
TCGA-AH-6547 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DF 
        1.45        78.12        15.02        13.05       126.44        24.13 
TCGA-DY-A1DG TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 
       51.48        18.28        37.51        31.30        32.19         0.69 

$`CTNNB1 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       14.50        16.83        15.39        10.39        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         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-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-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         0.49        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.05         6.97         4.73         7.17        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00        10.98        30.05        12.95        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       20.91         9.96        28.57         0.66        55.76        26.43 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.69             0.49 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          126.44           117.11 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           19.56            16.93 
[1] "0.7 - 126.4 (19.6)" "0.5 - 117.1 (16.9)"
[1] "hr=" "1.9"
D19V2, 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         4          3
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTNNB1 MUTATED            0          3        0         2
  CTNNB1 WILD-TYPE         15          7       13         4
D19V3, 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                4
  STAGE IIIA              1                3
  STAGE IIIB              0               15
  STAGE IIIC              3                7
  STAGE IV                0               13
  STAGE IVA               2                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
D19V4, 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
D19V5, 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"
D19V6, 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
D19V7, 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
D19V8, 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
D19V9, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    0 19
  CTNNB1 WILD-TYPE  4 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   19
  CTNNB1 WILD-TYPE    4   99
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               0                4
  YES             19               99
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  CTNNB1 MUTATED   11  0  0  1
  CTNNB1 WILD-TYPE 77  2  9  3
D19V10, 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"
D19V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED       0                         0    14
  CTNNB1 WILD-TYPE     1                         3    36
D19V12, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                 14               36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = KIAA1804 MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  KIAA1804 MUTATED    8  1
  KIAA1804 WILD-TYPE 88 17
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                105 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                 17 
$`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-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 
        0.99        15.95        19.99        19.99         7.99         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        19.96        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.99               0.49 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             61.97             126.44 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             36.03              16.83 
[1] "1.0 - 62.0 (36.0)"  "0.5 - 126.4 (16.8)"
[1] "hr=" "2.9"
D20V2, 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         4          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIAA1804 MUTATED            1          1        1         0
  KIAA1804 WILD-TYPE         14          9       12         6
D20V3, 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                  4
  STAGE IIIA                0                  4
  STAGE IIIB                1                 14
  STAGE IIIC                1                  9
  STAGE IV                  1                 12
  STAGE IVA                 0                  6
[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
D20V4, 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
D20V5, 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"
D20V6, 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
D20V7, 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
D20V8, 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
D20V9, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     0  10
  KIAA1804 WILD-TYPE   4 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      0   10
  KIAA1804 WILD-TYPE    4  108
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                 0                  4
  YES               10                108
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  KIAA1804 MUTATED    9  0  1  0
  KIAA1804 WILD-TYPE 79  2  8  4
D20V10, 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"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1804 MUTATED       0                         0     2
  KIAA1804 WILD-TYPE     1                         3    48
D20V12, multiclass
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 2                 52 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2692 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-2693         TCGA-AF-3400         TCGA-AF-3913 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AH-6544 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6549         TCGA-AH-6643 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AH-6644         TCGA-CI-6619         TCGA-CI-6620 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-CI-6621         TCGA-CI-6622         TCGA-CI-6624 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-EI-6510         TCGA-F5-6464         TCGA-F5-6465 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6811 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-G5-6641 
"KIAA1804 WILD-TYPE" 

Clustering(21) Variable = OXSM MUTATION ANALYSIS
D21V1, survival
                sevent
clus2             0  1
  OXSM MUTATED    4  0
  OXSM WILD-TYPE 92 18
  OXSM MUTATED OXSM WILD-TYPE 
             4            110 
  OXSM MUTATED OXSM WILD-TYPE 
             0             18 
$`OXSM MUTATED`
TCGA-AG-3892 TCGA-CL-5918 TCGA-DC-6682 TCGA-DT-5265 
       13.02         7.17        13.05         5.29 

$`OXSM WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 
        6.05         6.97         4.73        78.12        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        36.00        10.98        30.05        12.95        10.06 
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 
        0.49        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 
       37.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OXSM MUTATED OXSM WILD-TYPE 
          5.29           0.49 
  OXSM MUTATED OXSM WILD-TYPE 
         13.05         126.44 
  OXSM MUTATED OXSM WILD-TYPE 
        10.095         18.690 
[1] "5.3 - 13.1 (10.1)"  "0.5 - 126.4 (18.7)"
[1] "hr="     "9400000"
D21V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OXSM MUTATED            0          0        0         0
  OXSM WILD-TYPE         15         10       13         6
D21V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            0             15
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             0              6
[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
D21V4, 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
D21V5, 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"
D21V6, 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
D21V7, 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
D21V8, 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
D21V9, binary
                cls
clus               0   1
  OXSM MUTATED     0   4
  OXSM WILD-TYPE   4 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      0    4
  OXSM WILD-TYPE    4  114
     clus
vv    OXSM MUTATED OXSM WILD-TYPE
  NO             0              4
  YES            4            114
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  OXSM MUTATED    2  0  0  2
  OXSM WILD-TYPE 86  2  9  2
D21V10, 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"
D21V11, continuous
[1] "Remove cluster labels:" "OXSM MUTATED"          
clus
  OXSM MUTATED OXSM WILD-TYPE 
             2            111 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3893     TCGA-AG-3894 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6544 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6622 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6683 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-DY-A1DG     TCGA-DY-A1H8     TCGA-EI-6506     TCGA-EI-6507 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"OXSM WILD-TYPE" "OXSM WILD-TYPE" "OXSM WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXSM MUTATED       1                         0     2
  OXSM WILD-TYPE     0                         3    48
D21V12, multiclass
                           clus
vv                          OXSM MUTATED OXSM WILD-TYPE
  ASIAN                                1              0
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                2             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = BCL9 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2             0  1
  BCL9 MUTATED    3  2
  BCL9 WILD-TYPE 93 16
  BCL9 MUTATED BCL9 WILD-TYPE 
             5            109 
  BCL9 MUTATED BCL9 WILD-TYPE 
             2             16 
$`BCL9 MUTATED`
TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-4001 TCGA-AG-A002 TCGA-DY-A1DG 
       14.50        20.05        36.03        20.98        51.48 

$`BCL9 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        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         0.49         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BCL9 MUTATED BCL9 WILD-TYPE 
         14.50           0.49 
  BCL9 MUTATED BCL9 WILD-TYPE 
         51.48         126.44 
  BCL9 MUTATED BCL9 WILD-TYPE 
         20.98          17.03 
[1] "14.5 - 51.5 (21.0)" "0.5 - 126.4 (17.0)"
[1] "hr=" "1.9"
D22V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BCL9 MUTATED         1        0         1         0         0          0
  BCL9 WILD-TYPE      26        7        28         2         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9 MUTATED            0          0        1         2
  BCL9 WILD-TYPE         15         10       12         4
D22V3, multiclass
            clus
vv           BCL9 MUTATED BCL9 WILD-TYPE
  STAGE I               1             26
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              5
  STAGE IIIA            0              4
  STAGE IIIB            0             15
  STAGE IIIC            0             10
  STAGE IV              1             12
  STAGE IVA             2              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
  BCL9 MUTATED    0  1  3  1
  BCL9 WILD-TYPE  8 24 77  8
D22V4, multiclass
    clus
vv   BCL9 MUTATED BCL9 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
  BCL9 MUTATED    2  1  2
  BCL9 WILD-TYPE 65 31 19
D22V5, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  N0            2             65
  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"
D22V6, binary
                cls
clus              0  1
  BCL9 MUTATED    2  2
  BCL9 WILD-TYPE 90 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED      2    2
  BCL9 WILD-TYPE   90   15
   clus
vv  BCL9 MUTATED BCL9 WILD-TYPE
  0            2             90
  1            2             15
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus              0  1
  BCL9 MUTATED    1  4
  BCL9 WILD-TYPE 54 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED      1    4
  BCL9 WILD-TYPE   54   63
        clus
vv       BCL9 MUTATED BCL9 WILD-TYPE
  FEMALE            1             54
  MALE              4             63
[1] 2 2
[1] FALSE
D22V8, binary
                cls
clus               0   1
  BCL9 MUTATED     3   1
  BCL9 WILD-TYPE 103   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED      3    1
  BCL9 WILD-TYPE  103    9
                                clus
vv                               BCL9 MUTATED BCL9 WILD-TYPE
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 2 2
[1] FALSE
D22V9, binary
                cls
clus               0   1
  BCL9 MUTATED     0   5
  BCL9 WILD-TYPE   4 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED      0    5
  BCL9 WILD-TYPE    4  113
     clus
vv    BCL9 MUTATED BCL9 WILD-TYPE
  NO             0              4
  YES            5            113
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  BCL9 MUTATED    3  0  1  0
  BCL9 WILD-TYPE 85  2  8  4
D22V10, multiclass
    clus
vv   BCL9 MUTATED BCL9 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"
D22V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL9 MUTATED       0                         0     2
  BCL9 WILD-TYPE     1                         3    48
D22V12, multiclass
[1] "Remove cluster labels:" "BCL9 MUTATED"          
clus
  BCL9 MUTATED BCL9 WILD-TYPE 
             2             52 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-5654 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672     TCGA-AH-6544 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643     TCGA-AH-6644 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621     TCGA-CI-6622 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5337 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-DY-A1DF     TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" "BCL9 WILD-TYPE" 

Clustering(23) Variable = KRAS MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   52  7
  KRAS WILD-TYPE 44 11
  KRAS MUTATED KRAS WILD-TYPE 
            59             55 
  KRAS MUTATED KRAS WILD-TYPE 
             7             11 
$`KRAS MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       39.48        43.04        13.55        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         8.02         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         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-3902 
        0.99         0.99        36.95        13.02         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        28.04        14.04        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01W TCGA-AG-A020 
       25.97        23.01        15.95        36.03        70.03        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6549 
       49.97        61.97        41.00        38.04         0.49        17.49 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6160 
        0.72         6.05         6.97        78.12        13.97        30.05 
TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       10.06        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6235 
       18.28        31.30        28.57         0.66        55.76 

$`KRAS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-3574 
       24.13        19.10        12.72        10.39        15.39        36.03 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       32.02        36.03        24.00        46.03        34.03        50.04 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-3882 
        6.05        15.95        19.99        19.99        32.98        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4001 
        1.02        17.03        35.01        14.01        48.03        36.03 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
        1.02        20.98        37.02         9.07        12.00        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6619 
        1.94        38.96       117.11         1.45         0.69         6.05 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
        4.73         7.17        15.02        12.99        36.00        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6813 
       51.48        20.91         9.96        37.51        32.19         0.69 
TCGA-G5-6641 
       26.43 

  KRAS MUTATED KRAS WILD-TYPE 
          0.49           0.69 
  KRAS MUTATED KRAS WILD-TYPE 
         78.12         126.44 
  KRAS MUTATED KRAS WILD-TYPE 
         15.95          19.99 
[1] "0.5 - 78.1 (15.9)"  "0.7 - 126.4 (20.0)"
[1] "hr=" "1.3"
D23V2, 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         2          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED            7          4        6         4
  KRAS WILD-TYPE          8          6        7         2
D23V3, 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              2
  STAGE IIIA            3              1
  STAGE IIIB            7              8
  STAGE IIIC            4              6
  STAGE IV              6              7
  STAGE IVA             4              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
D23V4, 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
D23V5, 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"
D23V6, 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
D23V7, 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
D23V8, 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
D23V9, binary
                cls
clus              0  1
  KRAS MUTATED    1 62
  KRAS WILD-TYPE  3 56
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1   62
  KRAS WILD-TYPE    3   56
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             1              3
  YES           62             56
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   50  1  3  2
  KRAS WILD-TYPE 38  1  6  2
D23V10, 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"
D23V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0    26
  KRAS WILD-TYPE     1                         3    24
D23V12, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                               26             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = SLC12A6 MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2                0  1
  SLC12A6 MUTATED    6  0
  SLC12A6 WILD-TYPE 90 18
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                6               108 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                0                18 
$`SLC12A6 MUTATED`
TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6547 TCGA-CI-6622 TCGA-F5-6811 
       19.10        13.02        20.98         1.45         6.97        32.19 

$`SLC12A6 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         0.49        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.05         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       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         0.49 
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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
             1.45              0.49 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            32.19            126.44 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            16.06             17.26 
[1] "1.4 - 32.2 (16.1)"  "0.5 - 126.4 (17.3)"
[1] "hr="     "2.6e+07"
D24V2, 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         5          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLC12A6 MUTATED            0          0        0         0
  SLC12A6 WILD-TYPE         15         10       13         6
D24V3, 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                 5
  STAGE IIIA               0                 4
  STAGE IIIB               0                15
  STAGE IIIC               0                10
  STAGE IV                 0                13
  STAGE IVA                0                 6
[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
D24V4, 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
D24V5, 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"
D24V6, 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
D24V7, 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
D24V8, 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
D24V9, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED     0   6
  SLC12A6 WILD-TYPE   4 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED      0    6
  SLC12A6 WILD-TYPE    4  112
     clus
vv    SLC12A6 MUTATED SLC12A6 WILD-TYPE
  NO                0                 4
  YES               6               112
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  SLC12A6 MUTATED    2  0  0  0
  SLC12A6 WILD-TYPE 86  2  9  4
D24V10, multiclass
[1] "Remove cluster labels:" "SLC12A6 MUTATED"       
clus
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                2               101 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3893        TCGA-AG-3894 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A008 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A025 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-AG-A032        TCGA-AG-A036        TCGA-AH-6549        TCGA-AH-6643 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6812        TCGA-F5-6813        TCGA-G5-6235 
"SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" "SLC12A6 WILD-TYPE" 
       TCGA-G5-6641 
"SLC12A6 WILD-TYPE" 
D24V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC12A6 MUTATED       0                         0     4
  SLC12A6 WILD-TYPE     1                         3    46
D24V12, multiclass
                           clus
vv                          SLC12A6 MUTATED SLC12A6 WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   4                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = ZNF354C MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                0  1
  ZNF354C MUTATED    5  0
  ZNF354C WILD-TYPE 91 18
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                5               109 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                0                18 
$`ZNF354C MUTATED`
TCGA-AG-A002 TCGA-AH-6544 TCGA-EI-6507 TCGA-F5-6465 TCGA-F5-6813 
       20.98         0.49        19.96        37.51         0.69 

$`ZNF354C WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
        9.96        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  ZNF354C MUTATED ZNF354C WILD-TYPE 
             0.49              0.49 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            37.51            126.44 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            19.96             17.03 
[1] "0.5 - 37.5 (20.0)"  "0.5 - 126.4 (17.0)"
[1] "hr="     "2.6e+07"
D25V2, 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         5          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF354C MUTATED            0          1        0         0
  ZNF354C WILD-TYPE         15          9       13         6
D25V3, 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                 5
  STAGE IIIA               0                 4
  STAGE IIIB               0                15
  STAGE IIIC               1                 9
  STAGE IV                 0                13
  STAGE IVA                0                 6
[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
D25V4, 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
D25V5, 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"
D25V6, 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
D25V7, 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
D25V8, 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
D25V9, binary
                   cls
clus                  0   1
  ZNF354C MUTATED     0   5
  ZNF354C WILD-TYPE   4 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      0    5
  ZNF354C WILD-TYPE    4  113
     clus
vv    ZNF354C MUTATED ZNF354C WILD-TYPE
  NO                0                 4
  YES               5               113
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  ZNF354C MUTATED    4  0  0  0
  ZNF354C WILD-TYPE 84  2  9  4
D25V10, 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"
D25V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF354C MUTATED       0                         0     4
  ZNF354C WILD-TYPE     1                         3    46
D25V12, multiclass
                           clus
vv                          ZNF354C MUTATED ZNF354C WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   4                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = GABRP MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2              0  1
  GABRP MUTATED    4  0
  GABRP WILD-TYPE 92 18
  GABRP MUTATED GABRP WILD-TYPE 
              4             110 
  GABRP MUTATED GABRP WILD-TYPE 
              0              18 
$`GABRP MUTATED`
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A02N TCGA-EF-5830 
       32.98        13.02        61.97         0.49 

$`GABRP WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11         0.49         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        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 
       37.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GABRP MUTATED GABRP WILD-TYPE 
           0.49            0.49 
  GABRP MUTATED GABRP WILD-TYPE 
          61.97          126.44 
  GABRP MUTATED GABRP WILD-TYPE 
          23.00           17.26 
[1] "0.5 - 62.0 (23.0)"  "0.5 - 126.4 (17.3)"
[1] "hr="     "7.4e+07"
D26V2, 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         5          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABRP MUTATED            0          0        0         0
  GABRP WILD-TYPE         15         10       13         6
D26V3, 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               5
  STAGE IIIA             0               4
  STAGE IIIB             0              15
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               6
[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
D26V4, 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
D26V5, 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"
D26V6, 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
D26V7, 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
D26V8, 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
D26V9, binary
                 cls
clus                0   1
  GABRP MUTATED     0   4
  GABRP WILD-TYPE   4 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      0    4
  GABRP WILD-TYPE    4  114
     clus
vv    GABRP MUTATED GABRP WILD-TYPE
  NO              0               4
  YES             4             114
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  GABRP MUTATED    4  0  0  0
  GABRP WILD-TYPE 84  2  9  4
D26V10, 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"
D26V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GABRP MUTATED       0                         0     1
  GABRP WILD-TYPE     1                         3    49
D26V12, multiclass
[1] "Remove cluster labels:" "GABRP MUTATED"         
clus
  GABRP MUTATED GABRP WILD-TYPE 
              1              53 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235 
"GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" "GABRP WILD-TYPE" 
     TCGA-G5-6641 
"GABRP WILD-TYPE" 

Clustering(27) Variable = BRAF MUTATION ANALYSIS
D27V1, survival
                sevent
clus2             0  1
  BRAF MUTATED    9  2
  BRAF WILD-TYPE 87 16
  BRAF MUTATED BRAF WILD-TYPE 
            11            103 
  BRAF MUTATED BRAF WILD-TYPE 
             2             16 
$`BRAF MUTATED`
TCGA-AG-3578 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       32.02        10.98        30.05        12.95        10.06         5.29 
TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6811 
       57.24         0.49        20.91        18.28        32.19 

$`BRAF WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.99        13.97        36.00        13.05       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-F5-6464 
       24.13        51.48        32.61        20.55        19.96         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       37.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BRAF MUTATED BRAF WILD-TYPE 
          0.49           0.49 
  BRAF MUTATED BRAF WILD-TYPE 
         57.24         126.44 
  BRAF MUTATED BRAF WILD-TYPE 
         18.28          17.03 
[1] "0.5 - 57.2 (18.3)"  "0.5 - 126.4 (17.0)"
[1] "hr=" "1.3"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BRAF MUTATED         2        1         2         1         0          0
  BRAF WILD-TYPE      25        6        27         1         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED            4          0        0         2
  BRAF WILD-TYPE         11         10       13         4
D27V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               2             25
  STAGE II              1              6
  STAGE IIA             2             27
  STAGE IIB             1              1
  STAGE III             0              5
  STAGE IIIA            0              4
  STAGE IIIB            4             11
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             2              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  3  8  1
  BRAF WILD-TYPE  8 22 72  8
D27V4, multiclass
    clus
vv   BRAF MUTATED BRAF 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
  BRAF MUTATED    7  4  1
  BRAF WILD-TYPE 60 28 20
D27V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0            7             60
  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   10  1
  BRAF WILD-TYPE 82 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10    1
  BRAF WILD-TYPE   82   16
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           10             82
  1            1             16
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus              0  1
  BRAF MUTATED    7  5
  BRAF WILD-TYPE 48 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      7    5
  BRAF WILD-TYPE   48   62
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            7             48
  MALE              5             62
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus              0  1
  BRAF MUTATED   10  2
  BRAF WILD-TYPE 96  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10    2
  BRAF WILD-TYPE   96    8
                                clus
vv                               BRAF MUTATED BRAF WILD-TYPE
  RECTAL ADENOCARCINOMA                    10             96
  RECTAL MUCINOUS ADENOCARCINOMA            2              8
[1] 2 2
[1] FALSE
D27V9, binary
                cls
clus               0   1
  BRAF MUTATED     0  12
  BRAF WILD-TYPE   4 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0   12
  BRAF WILD-TYPE    4  106
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             0              4
  YES           12            106
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  BRAF MUTATED    9  0  0  1
  BRAF WILD-TYPE 79  2  9  3
D27V10, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0            9             79
  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
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       1                         0     9
  BRAF WILD-TYPE     0                         3    41
D27V12, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                1              0
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                9             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = PIK3CA MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   32  3
  PIK3CA WILD-TYPE 64 15
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              35               79 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               3               15 
$`PIK3CA MUTATED`
TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-3742 
       24.13        19.10        15.39        10.39         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-A00H TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6544 
        0.99        36.95        25.97        10.98        61.97         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        7.17        12.99        36.00        10.98        30.05        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5830 
       10.06         5.29       126.44        41.36        51.48         0.49 
TCGA-EI-6507 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       19.96        31.30        32.19         0.69        55.76 

$`PIK3CA WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       16.83        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       15.95        19.99        19.99         7.99         0.99        32.98 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       70.03        64.01        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6620 TCGA-DC-5337 
       38.04       117.11         1.45        17.49         6.05        15.02 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 
       13.97        12.95        57.24        24.13        32.61        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6812 
       20.91        18.28         9.96        37.51        28.57         0.66 
TCGA-G5-6641 
       26.43 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.49             0.66 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          126.44           117.11 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           12.99            19.99 
[1] "0.5 - 126.4 (13.0)" "0.7 - 117.1 (20.0)"
[1] "hr=" "2.3"
D28V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PIK3CA MUTATED         7        2        10         2         1          0
  PIK3CA WILD-TYPE      20        5        19         0         4          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIK3CA MUTATED            5          4        3         1
  PIK3CA WILD-TYPE         10          6       10         5
D28V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 7               20
  STAGE II                2                5
  STAGE IIA              10               19
  STAGE IIB               2                0
  STAGE III               1                4
  STAGE IIIA              0                4
  STAGE IIIB              5               10
  STAGE IIIC              4                6
  STAGE IV                3               10
  STAGE IVA               1                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
  PIK3CA MUTATED    1  6 26  4
  PIK3CA WILD-TYPE  7 19 54  5
D28V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1                7
  T2              6               19
  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   21 10  5
  PIK3CA WILD-TYPE 46 22 16
D28V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             21               46
  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"
D28V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED   26  4
  PIK3CA WILD-TYPE 66 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     26    4
  PIK3CA WILD-TYPE   66   13
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             26               66
  1              4               13
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED   13 24
  PIK3CA WILD-TYPE 42 43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     13   24
  PIK3CA WILD-TYPE   42   43
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             13               42
  MALE               24               43
[1] 2 2
[1] FALSE
D28V8, binary
                  cls
clus                0  1
  PIK3CA MUTATED   32  4
  PIK3CA WILD-TYPE 74  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     32    4
  PIK3CA WILD-TYPE   74    6
                                clus
vv                               PIK3CA MUTATED PIK3CA WILD-TYPE
  RECTAL ADENOCARCINOMA                      32               74
  RECTAL MUCINOUS ADENOCARCINOMA              4                6
[1] 2 2
[1] FALSE
D28V9, binary
                  cls
clus                0  1
  PIK3CA MUTATED    3 34
  PIK3CA WILD-TYPE  1 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3   34
  PIK3CA WILD-TYPE    1   84
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               3                1
  YES             34               84
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  PIK3CA MUTATED   20  1  1  3
  PIK3CA WILD-TYPE 68  1  8  1
D28V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             20               68
  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"
D28V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       1                         2    25
  PIK3CA WILD-TYPE     0                         1    25
D28V12, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  1                0
  BLACK OR AFRICAN AMERICAN              2                1
  WHITE                                 25               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = CEP290 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  CEP290 MUTATED    6  0
  CEP290 WILD-TYPE 90 18
  CEP290 MUTATED CEP290 WILD-TYPE 
               6              108 
  CEP290 MUTATED CEP290 WILD-TYPE 
               0               18 
$`CEP290 MUTATED`
TCGA-AF-6655 TCGA-AG-3898 TCGA-AH-6549 TCGA-CI-6619 TCGA-DY-A0XA TCGA-G5-6641 
       20.02        48.03        17.49         6.05       126.44        26.43 

$`CEP290 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.45         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
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         0.49 
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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 

  CEP290 MUTATED CEP290 WILD-TYPE 
            6.05             0.49 
  CEP290 MUTATED CEP290 WILD-TYPE 
          126.44           117.11 
  CEP290 MUTATED CEP290 WILD-TYPE 
          23.225           16.930 
[1] "6.0 - 126.4 (23.2)" "0.5 - 117.1 (16.9)"
[1] "hr="     "7.7e+07"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  CEP290 MUTATED         0        0         2         0         0          2
  CEP290 WILD-TYPE      27        7        27         2         5          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CEP290 MUTATED            0          0        1         0
  CEP290 WILD-TYPE         15         10       12         6
D29V3, multiclass
            clus
vv           CEP290 MUTATED CEP290 WILD-TYPE
  STAGE I                 0               27
  STAGE II                0                7
  STAGE IIA               2               27
  STAGE IIB               0                2
  STAGE III               0                5
  STAGE IIIA              2                2
  STAGE IIIB              0               15
  STAGE IIIC              0               10
  STAGE IV                1               12
  STAGE IVA               0                6
[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
  CEP290 MUTATED    1  1  4  0
  CEP290 WILD-TYPE  7 24 76  9
D29V4, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  T1              1                7
  T2              1               24
  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
  CEP290 MUTATED    2  3  0
  CEP290 WILD-TYPE 65 29 21
D29V5, multiclass
    clus
vv   CEP290 MUTATED CEP290 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"
D29V6, binary
                  cls
clus                0  1
  CEP290 MUTATED    3  1
  CEP290 WILD-TYPE 89 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      3    1
  CEP290 WILD-TYPE   89   16
   clus
vv  CEP290 MUTATED CEP290 WILD-TYPE
  0              3               89
  1              1               16
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                0  1
  CEP290 MUTATED    1  5
  CEP290 WILD-TYPE 54 62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      1    5
  CEP290 WILD-TYPE   54   62
        clus
vv       CEP290 MUTATED CEP290 WILD-TYPE
  FEMALE              1               54
  MALE                5               62
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                 0   1
  CEP290 MUTATED     5   1
  CEP290 WILD-TYPE 101   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      5    1
  CEP290 WILD-TYPE  101    9
                                clus
vv                               CEP290 MUTATED CEP290 WILD-TYPE
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 2 2
[1] FALSE
D29V9, binary
                  cls
clus                 0   1
  CEP290 MUTATED     0   6
  CEP290 WILD-TYPE   4 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      0    6
  CEP290 WILD-TYPE    4  112
     clus
vv    CEP290 MUTATED CEP290 WILD-TYPE
  NO               0                4
  YES              6              112
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  CEP290 MUTATED    3  0  0  1
  CEP290 WILD-TYPE 85  2  9  3
D29V10, multiclass
    clus
vv   CEP290 MUTATED CEP290 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"
D29V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP290 MUTATED       0                         0     5
  CEP290 WILD-TYPE     1                         3    45
D29V12, multiclass
                           clus
vv                          CEP290 MUTATED CEP290 WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  5               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = LIG1 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2             0  1
  LIG1 MUTATED    4  0
  LIG1 WILD-TYPE 92 18
  LIG1 MUTATED LIG1 WILD-TYPE 
             4            110 
  LIG1 MUTATED LIG1 WILD-TYPE 
             0             18 
$`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-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.99        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6464 
       51.48        32.61         0.49        20.55        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LIG1 MUTATED LIG1 WILD-TYPE 
         13.97           0.49 
  LIG1 MUTATED LIG1 WILD-TYPE 
         32.98         126.44 
  LIG1 MUTATED LIG1 WILD-TYPE 
         19.12          17.03 
[1] "14.0 - 33.0 (19.1)" "0.5 - 126.4 (17.0)"
[1] "hr="     "2.6e+07"
D30V2, 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         5          3
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIG1 MUTATED            0          0        0         1
  LIG1 WILD-TYPE         15         10       13         5
D30V3, 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              5
  STAGE IIIA            1              3
  STAGE IIIB            0             15
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             1              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
D30V4, 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
D30V5, 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"
D30V6, 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
D30V7, 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
D30V8, 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
D30V9, binary
                cls
clus               0   1
  LIG1 MUTATED     0   4
  LIG1 WILD-TYPE   4 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      0    4
  LIG1 WILD-TYPE    4  114
     clus
vv    LIG1 MUTATED LIG1 WILD-TYPE
  NO             0              4
  YES            4            114
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  LIG1 MUTATED    4  0  0  0
  LIG1 WILD-TYPE 84  2  9  4
D30V10, 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"
D30V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIG1 MUTATED       0                         0     3
  LIG1 WILD-TYPE     1                         3    47
D30V12, multiclass
                           clus
vv                          LIG1 MUTATED LIG1 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = PCBP1 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2              0  1
  PCBP1 MUTATED    4  0
  PCBP1 WILD-TYPE 92 18
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             110 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              18 
$`PCBP1 MUTATED`
TCGA-AG-3894 TCGA-AH-6544 TCGA-CI-6622 TCGA-F5-6465 
       14.01         0.49         6.97        37.51 

$`PCBP1 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       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         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
           0.49            0.49 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          37.51          126.44 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
         10.490          17.885 
[1] "0.5 - 37.5 (10.5)"  "0.5 - 126.4 (17.9)"
[1] "hr="     "2.5e+07"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCBP1 MUTATED         0        0         2         1         0          0
  PCBP1 WILD-TYPE      27        7        27         1         5          4
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED            0          0        0         0
  PCBP1 WILD-TYPE         15         10       13         6
D31V3, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                0              27
  STAGE II               0               7
  STAGE IIA              2              27
  STAGE IIB              1               1
  STAGE III              0               5
  STAGE IIIA             0               4
  STAGE IIIB             0              15
  STAGE IIIC             0              10
  STAGE IV               0              13
  STAGE IVA              0               6
[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  0  3  1
  PCBP1 WILD-TYPE  8 25 77  8
D31V4, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               8
  T2             0              25
  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    3  1  0
  PCBP1 WILD-TYPE 64 31 21
D31V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 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"
D31V6, binary
                 cls
clus               0  1
  PCBP1 MUTATED    3  1
  PCBP1 WILD-TYPE 89 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      3    1
  PCBP1 WILD-TYPE   89   16
   clus
vv  PCBP1 MUTATED PCBP1 WILD-TYPE
  0             3              89
  1             1              16
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus               0  1
  PCBP1 MUTATED    1  3
  PCBP1 WILD-TYPE 54 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      1    3
  PCBP1 WILD-TYPE   54   64
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             1              54
  MALE               3              64
[1] 2 2
[1] FALSE
D31V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     4   0
  PCBP1 WILD-TYPE 102  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      4    0
  PCBP1 WILD-TYPE  102   10
                                clus
vv                               PCBP1 MUTATED PCBP1 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
D31V9, binary
                 cls
clus                0   1
  PCBP1 MUTATED     0   4
  PCBP1 WILD-TYPE   4 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      0    4
  PCBP1 WILD-TYPE    4  114
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  NO              0               4
  YES             4             114
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  PCBP1 MUTATED    2  0  0  0
  PCBP1 WILD-TYPE 86  2  9  4
D31V10, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2             101 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036      TCGA-AH-6549 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918      TCGA-DC-5337 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6571 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-G5-6641 
"PCBP1 WILD-TYPE" 
D31V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCBP1 MUTATED       0                         0     3
  PCBP1 WILD-TYPE     1                         3    47
D31V12, multiclass
                           clus
vv                          PCBP1 MUTATED PCBP1 WILD-TYPE
  ASIAN                                 0               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = ATP8B1 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2               0  1
  ATP8B1 MUTATED    5  0
  ATP8B1 WILD-TYPE 91 18
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               5              109 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               0               18 
$`ATP8B1 MUTATED`
TCGA-AG-3605 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6643 TCGA-F5-6812 
        0.99        13.02        20.98         0.69         0.66 

$`ATP8B1 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         6.05        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11         0.49         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
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 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       37.51        31.30        28.57        32.19         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            0.66             0.49 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
           20.98           126.44 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            0.99            18.28 
[1] "0.7 - 21.0 (1.0)"   "0.5 - 126.4 (18.3)"
[1] "hr="     "9200000"
D32V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ATP8B1 MUTATED         2        0         1         0         0          0
  ATP8B1 WILD-TYPE      25        7        28         2         5          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATP8B1 MUTATED            0          1        1         0
  ATP8B1 WILD-TYPE         15          9       12         6
D32V3, multiclass
            clus
vv           ATP8B1 MUTATED ATP8B1 WILD-TYPE
  STAGE I                 2               25
  STAGE II                0                7
  STAGE IIA               1               28
  STAGE IIB               0                2
  STAGE III               0                5
  STAGE IIIA              0                4
  STAGE IIIB              0               15
  STAGE IIIC              1                9
  STAGE IV                1               12
  STAGE IVA               0                6
[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
  ATP8B1 MUTATED    1  1  3  0
  ATP8B1 WILD-TYPE  7 24 77  9
D32V4, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  T1              1                7
  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
  ATP8B1 MUTATED    3  1  1
  ATP8B1 WILD-TYPE 64 31 20
D32V5, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 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"
D32V6, binary
                  cls
clus                0  1
  ATP8B1 MUTATED    4  1
  ATP8B1 WILD-TYPE 88 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED      4    1
  ATP8B1 WILD-TYPE   88   16
   clus
vv  ATP8B1 MUTATED ATP8B1 WILD-TYPE
  0              4               88
  1              1               16
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                0  1
  ATP8B1 MUTATED    2  3
  ATP8B1 WILD-TYPE 53 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED      2    3
  ATP8B1 WILD-TYPE   53   64
        clus
vv       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  FEMALE              2               53
  MALE                3               64
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED     5   0
  ATP8B1 WILD-TYPE 101  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED      5    0
  ATP8B1 WILD-TYPE  101   10
                                clus
vv                               ATP8B1 MUTATED ATP8B1 WILD-TYPE
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
D32V9, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED     0   5
  ATP8B1 WILD-TYPE   4 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED      0    5
  ATP8B1 WILD-TYPE    4  113
     clus
vv    ATP8B1 MUTATED ATP8B1 WILD-TYPE
  NO               0                4
  YES              5              113
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  ATP8B1 MUTATED    4  0  1  0
  ATP8B1 WILD-TYPE 84  2  8  4
D32V10, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  R0              4               84
  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"
D32V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP8B1 MUTATED       0                         0     2
  ATP8B1 WILD-TYPE     1                         3    48
D32V12, multiclass
[1] "Remove cluster labels:" "ATP8B1 MUTATED"        
clus
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               2               52 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6644 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621       TCGA-CI-6622 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918       TCGA-DC-5337 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157       TCGA-DC-6158 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682       TCGA-DC-6683 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EF-5830 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-F5-6811       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 

Clustering(33) Variable = FLT1 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2             0  1
  FLT1 MUTATED    6  2
  FLT1 WILD-TYPE 90 16
  FLT1 MUTATED FLT1 WILD-TYPE 
             8            106 
  FLT1 MUTATED FLT1 WILD-TYPE 
             2             16 
$`FLT1 MUTATED`
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3878 TCGA-AG-A002 TCGA-DY-A0XA 
       14.50        16.83        15.39         0.99        20.98       126.44 
TCGA-DY-A1DD TCGA-EI-6507 
       57.24        19.96 

$`FLT1 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11         0.49         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        37.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FLT1 MUTATED FLT1 WILD-TYPE 
          0.99           0.49 
  FLT1 MUTATED FLT1 WILD-TYPE 
        126.44         117.11 
  FLT1 MUTATED FLT1 WILD-TYPE 
        18.395         17.260 
[1] "1.0 - 126.4 (18.4)" "0.5 - 117.1 (17.3)"
[1] "hr=" "1.1"
D33V2, 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         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLT1 MUTATED            2          0        0         1
  FLT1 WILD-TYPE         13         10       13         5
D33V3, 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              5
  STAGE IIIA            0              4
  STAGE IIIB            2             13
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             1              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
  FLT1 MUTATED    0  3  4  1
  FLT1 WILD-TYPE  8 22 76  8
D33V4, 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
D33V5, 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"
D33V6, 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
D33V7, 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
D33V8, 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
D33V9, binary
                cls
clus               0   1
  FLT1 MUTATED     1   7
  FLT1 WILD-TYPE   3 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED      1    7
  FLT1 WILD-TYPE    3  111
     clus
vv    FLT1 MUTATED FLT1 WILD-TYPE
  NO             1              3
  YES            7            111
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  FLT1 MUTATED    5  0  0  0
  FLT1 WILD-TYPE 83  2  9  4
D33V10, 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"
D33V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLT1 MUTATED       0                         0     6
  FLT1 WILD-TYPE     1                         3    44
D33V12, multiclass
                           clus
vv                          FLT1 MUTATED FLT1 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                6             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = OBSCN MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2              0  1
  OBSCN MUTATED   11  1
  OBSCN WILD-TYPE 85 17
  OBSCN MUTATED OBSCN WILD-TYPE 
             12             102 
  OBSCN MUTATED OBSCN WILD-TYPE 
              1              17 
$`OBSCN MUTATED`
TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A026 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6624 
       19.10        13.02         1.94         0.49         0.69         4.73 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6155 TCGA-EI-6507 TCGA-F5-6465 TCGA-G5-6235 
       78.12        15.02        13.97        19.96        37.51        55.76 

$`OBSCN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        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         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-5869 
        0.72         6.05         6.05         6.97         7.17        12.99 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       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         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  OBSCN MUTATED OBSCN WILD-TYPE 
           0.49            0.49 
  OBSCN MUTATED OBSCN WILD-TYPE 
          78.12          126.44 
  OBSCN MUTATED OBSCN WILD-TYPE 
         14.495          17.885 
[1] "0.5 - 78.1 (14.5)"  "0.5 - 126.4 (17.9)"
[1] "hr=" "2"  
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  OBSCN MUTATED         4        1         3         0         0          1
  OBSCN WILD-TYPE      23        6        26         2         5          3
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OBSCN MUTATED            1          2        0         0
  OBSCN WILD-TYPE         14          8       13         6
D34V3, multiclass
            clus
vv           OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I                4              23
  STAGE II               1               6
  STAGE IIA              3              26
  STAGE IIB              0               2
  STAGE III              0               5
  STAGE IIIA             1               3
  STAGE IIIB             1              14
  STAGE IIIC             2               8
  STAGE IV               0              13
  STAGE IVA              0               6
[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
  OBSCN MUTATED    2  3  7  1
  OBSCN WILD-TYPE  6 22 73  8
D34V4, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  T1             2               6
  T2             3              22
  T3             7              73
  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
  OBSCN MUTATED    8  3  2
  OBSCN WILD-TYPE 59 29 19
D34V5, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  N0             8              59
  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"
D34V6, binary
                 cls
clus               0  1
  OBSCN MUTATED    9  1
  OBSCN WILD-TYPE 83 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      9    1
  OBSCN WILD-TYPE   83   16
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0             9              83
  1             1              16
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus               0  1
  OBSCN MUTATED    6  7
  OBSCN WILD-TYPE 49 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      6    7
  OBSCN WILD-TYPE   49   60
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  FEMALE             6              49
  MALE               7              60
[1] 2 2
[1] FALSE
D34V8, binary
                 cls
clus               0  1
  OBSCN MUTATED   11  0
  OBSCN WILD-TYPE 95 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     11    0
  OBSCN WILD-TYPE   95   10
                                clus
vv                               OBSCN MUTATED OBSCN WILD-TYPE
  RECTAL ADENOCARCINOMA                     11              95
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 2 2
[1] FALSE
D34V9, binary
                 cls
clus                0   1
  OBSCN MUTATED     0  13
  OBSCN WILD-TYPE   4 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      0   13
  OBSCN WILD-TYPE    4  105
     clus
vv    OBSCN MUTATED OBSCN WILD-TYPE
  NO              0               4
  YES            13             105
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2 RX
  OBSCN MUTATED    6  2  0  1
  OBSCN WILD-TYPE 82  0  9  3
D34V10, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  R0             6              82
  R1             2               0
  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"
D34V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OBSCN MUTATED       0                         0    10
  OBSCN WILD-TYPE     1                         3    40
D34V12, multiclass
                           clus
vv                          OBSCN MUTATED OBSCN WILD-TYPE
  ASIAN                                 0               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                10              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = VANGL1 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2               0  1
  VANGL1 MUTATED    2  1
  VANGL1 WILD-TYPE 94 17
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3              111 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               1               17 
$`VANGL1 MUTATED`
TCGA-AF-5654 TCGA-AG-3731 TCGA-F5-6465 
       16.83         1.02        37.51 

$`VANGL1 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        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        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  VANGL1 MUTATED VANGL1 WILD-TYPE 
            1.02             0.49 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
           37.51           126.44 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
           16.83            17.49 
[1] "1.0 - 37.5 (16.8)"  "0.5 - 126.4 (17.5)"
[1] "hr=" "3"  
D35V2, 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         5          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VANGL1 MUTATED            0          0        1         0
  VANGL1 WILD-TYPE         15         10       12         6
D35V3, 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                5
  STAGE IIIA              0                4
  STAGE IIIB              0               15
  STAGE IIIC              0               10
  STAGE IV                1               12
  STAGE IVA               0                6
[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
D35V4, 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
D35V5, 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"
D35V6, 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
D35V7, 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
D35V8, 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
D35V9, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     0   3
  VANGL1 WILD-TYPE   4 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      0    3
  VANGL1 WILD-TYPE    4  115
     clus
vv    VANGL1 MUTATED VANGL1 WILD-TYPE
  NO               0                4
  YES              3              115
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  VANGL1 MUTATED    2  0  1  0
  VANGL1 WILD-TYPE 86  2  8  4
D35V10, 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"
D35V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VANGL1 MUTATED       0                         0     2
  VANGL1 WILD-TYPE     1                         3    48
D35V12, multiclass
[1] "Remove cluster labels:" "VANGL1 MUTATED"        
clus
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               2               52 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672       TCGA-AH-6544 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643       TCGA-AH-6644 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621       TCGA-CI-6622 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918       TCGA-DC-5337 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157       TCGA-DC-6158 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682       TCGA-DC-6683 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EF-5830 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6464       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" "VANGL1 WILD-TYPE" 

Clustering(36) Variable = RRP8 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2             0  1
  RRP8 MUTATED    4  1
  RRP8 WILD-TYPE 92 17
  RRP8 MUTATED RRP8 WILD-TYPE 
             5            109 
  RRP8 MUTATED RRP8 WILD-TYPE 
             1             17 
$`RRP8 MUTATED`
TCGA-AG-A01Y TCGA-AG-A036 TCGA-CL-5918 TCGA-DY-A1DC TCGA-EI-6507 
       64.01       117.11         7.17        41.36        19.96 

$`RRP8 WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       36.03         9.07        12.00        70.03        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RRP8 MUTATED RRP8 WILD-TYPE 
          7.17           0.49 
  RRP8 MUTATED RRP8 WILD-TYPE 
        117.11         126.44 
  RRP8 MUTATED RRP8 WILD-TYPE 
         41.36          17.03 
[1] "7.2 - 117.1 (41.4)" "0.5 - 126.4 (17.0)"
[1] "hr=" "2.2"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RRP8 MUTATED         0        1         3         0         1          0
  RRP8 WILD-TYPE      27        6        26         2         4          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRP8 MUTATED            0          0        0         0
  RRP8 WILD-TYPE         15         10       13         6
D36V3, multiclass
            clus
vv           RRP8 MUTATED RRP8 WILD-TYPE
  STAGE I               0             27
  STAGE II              1              6
  STAGE IIA             3             26
  STAGE IIB             0              2
  STAGE III             1              4
  STAGE IIIA            0              4
  STAGE IIIB            0             15
  STAGE IIIC            0             10
  STAGE IV              0             13
  STAGE IVA             0              6
[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
  RRP8 MUTATED    0  0  5  0
  RRP8 WILD-TYPE  8 25 75  9
D36V4, multiclass
    clus
vv   RRP8 MUTATED RRP8 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
  RRP8 MUTATED    4  0  1
  RRP8 WILD-TYPE 63 32 20
D36V5, multiclass
    clus
vv   RRP8 MUTATED RRP8 WILD-TYPE
  N0            4             63
  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"
D36V6, binary
                cls
clus              0  1
  RRP8 MUTATED    4  0
  RRP8 WILD-TYPE 88 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP8 MUTATED      4    0
  RRP8 WILD-TYPE   88   17
   clus
vv  RRP8 MUTATED RRP8 WILD-TYPE
  0            4             88
  1            0             17
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus              0  1
  RRP8 MUTATED    3  2
  RRP8 WILD-TYPE 52 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP8 MUTATED      3    2
  RRP8 WILD-TYPE   52   65
        clus
vv       RRP8 MUTATED RRP8 WILD-TYPE
  FEMALE            3             52
  MALE              2             65
[1] 2 2
[1] FALSE
D36V8, binary
                cls
clus               0   1
  RRP8 MUTATED     5   0
  RRP8 WILD-TYPE 101  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP8 MUTATED      5    0
  RRP8 WILD-TYPE  101   10
                                clus
vv                               RRP8 MUTATED RRP8 WILD-TYPE
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
D36V9, binary
                cls
clus               0   1
  RRP8 MUTATED     0   5
  RRP8 WILD-TYPE   4 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP8 MUTATED      0    5
  RRP8 WILD-TYPE    4  113
     clus
vv    RRP8 MUTATED RRP8 WILD-TYPE
  NO             0              4
  YES            5            113
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  RRP8 MUTATED    3  0  0  1
  RRP8 WILD-TYPE 85  2  9  3
D36V10, multiclass
    clus
vv   RRP8 MUTATED RRP8 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"
D36V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RRP8 MUTATED       0                         0     3
  RRP8 WILD-TYPE     1                         3    47
D36V12, multiclass
                           clus
vv                          RRP8 MUTATED RRP8 WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = AGL MUTATION ANALYSIS
D37V1, survival
               sevent
clus2            0  1
  AGL MUTATED    3  0
  AGL WILD-TYPE 93 18
  AGL MUTATED AGL WILD-TYPE 
            3           111 
  AGL MUTATED AGL WILD-TYPE 
            0            18 
$`AGL MUTATED`
TCGA-AG-3731 TCGA-AG-A002 TCGA-EI-6507 
        1.02        20.98        19.96 

$`AGL WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AGL MUTATED AGL WILD-TYPE 
         1.02          0.49 
  AGL MUTATED AGL WILD-TYPE 
        20.98        126.44 
  AGL MUTATED AGL WILD-TYPE 
        19.96         17.03 
[1] "1.0 - 21.0 (20.0)"  "0.5 - 126.4 (17.0)"
[1] "hr="     "9200000"
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         5          4
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGL MUTATED            1          0        1         0
  AGL WILD-TYPE         14         10       12         6
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             5
  STAGE IIIA           0             4
  STAGE IIIB           1            14
  STAGE IIIC           0            10
  STAGE IV             1            12
  STAGE IVA            0             6
[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     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
D37V9, binary
               cls
clus              0   1
  AGL MUTATED     0   4
  AGL WILD-TYPE   4 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGL MUTATED      0    4
  AGL WILD-TYPE    4  114
     clus
vv    AGL MUTATED AGL WILD-TYPE
  NO            0             4
  YES           4           114
[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
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AGL MUTATED       0                         0     1
  AGL WILD-TYPE     1                         3    49
D37V12, multiclass
[1] "Remove cluster labels:" "AGL MUTATED"           
clus
  AGL MUTATED AGL WILD-TYPE 
            1            53 
   TCGA-AF-2687    TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-2693 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AF-3400    TCGA-AF-3913    TCGA-AF-4110    TCGA-AF-5654    TCGA-AF-6136 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AF-6655    TCGA-AF-6672    TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-AH-6643    TCGA-AH-6644    TCGA-CI-6619    TCGA-CI-6620    TCGA-CI-6621 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-CI-6622    TCGA-CI-6624    TCGA-CL-5917    TCGA-CL-5918    TCGA-DC-5337 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-5869    TCGA-DC-6155    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6160 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DC-6681    TCGA-DC-6682    TCGA-DC-6683    TCGA-DT-5265    TCGA-DY-A0XA 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DF    TCGA-DY-A1DG    TCGA-DY-A1H8 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-EF-5830    TCGA-EI-6506    TCGA-EI-6508    TCGA-EI-6510    TCGA-F5-6464 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702    TCGA-F5-6811    TCGA-F5-6812 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 
   TCGA-F5-6813    TCGA-G5-6235    TCGA-G5-6641 
"AGL WILD-TYPE" "AGL WILD-TYPE" "AGL WILD-TYPE" 

Clustering(38) Variable = RLIM MUTATION ANALYSIS
D38V1, survival
                sevent
clus2             0  1
  RLIM MUTATED    2  1
  RLIM WILD-TYPE 94 17
  RLIM MUTATED RLIM WILD-TYPE 
             3            111 
  RLIM MUTATED RLIM WILD-TYPE 
             1             17 
$`RLIM MUTATED`
TCGA-AF-2687 TCGA-DY-A0XA TCGA-DY-A1DG 
       24.13       126.44        51.48 

$`RLIM WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-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 
        0.49         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06         5.29        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        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        37.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RLIM MUTATED RLIM WILD-TYPE 
         24.13           0.49 
  RLIM MUTATED RLIM WILD-TYPE 
        126.44         117.11 
  RLIM MUTATED RLIM WILD-TYPE 
         51.48          17.03 
[1] "24.1 - 126.4 (51.5)" "0.5 - 117.1 (17.0)" 
[1] "hr=" "1.5"
D38V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  RLIM MUTATED         0        0         1         0         0          0
  RLIM WILD-TYPE      27        7        28         2         5          4
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RLIM MUTATED            0          1        0         1
  RLIM WILD-TYPE         15          9       13         5
D38V3, multiclass
            clus
vv           RLIM MUTATED RLIM WILD-TYPE
  STAGE I               0             27
  STAGE II              0              7
  STAGE IIA             1             28
  STAGE IIB             0              2
  STAGE III             0              5
  STAGE IIIA            0              4
  STAGE IIIB            0             15
  STAGE IIIC            1              9
  STAGE IV              0             13
  STAGE IVA             1              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
  RLIM MUTATED    0  0  3  0
  RLIM WILD-TYPE  8 25 77  9
D38V4, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            0              8
  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
  RLIM MUTATED    1  1  1
  RLIM WILD-TYPE 66 31 20
D38V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0            1             66
  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"
D38V6, binary
                cls
clus              0  1
  RLIM MUTATED    2  1
  RLIM WILD-TYPE 90 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      2    1
  RLIM WILD-TYPE   90   16
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0            2             90
  1            1             16
[1] 2 2
[1] FALSE
D38V7, binary
                cls
clus              0  1
  RLIM MUTATED    1  2
  RLIM WILD-TYPE 54 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      1    2
  RLIM WILD-TYPE   54   65
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  FEMALE            1             54
  MALE              2             65
[1] 2 2
[1] FALSE
D38V8, binary
                cls
clus               0   1
  RLIM MUTATED     3   0
  RLIM WILD-TYPE 103  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      3    0
  RLIM WILD-TYPE  103   10
                                clus
vv                               RLIM MUTATED RLIM WILD-TYPE
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 2 2
[1] FALSE
D38V9, binary
                cls
clus               0   1
  RLIM MUTATED     1   2
  RLIM WILD-TYPE   3 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      1    2
  RLIM WILD-TYPE    3  116
     clus
vv    RLIM MUTATED RLIM WILD-TYPE
  NO             1              3
  YES            2            116
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  RLIM MUTATED    1  0  0  0
  RLIM WILD-TYPE 87  2  9  4
D38V10, multiclass
[1] "Remove cluster labels:" "RLIM MUTATED"          
clus
  RLIM MUTATED RLIM WILD-TYPE 
             1            102 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6655 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6549 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5337 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812     TCGA-F5-6813 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" "RLIM WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"RLIM WILD-TYPE" "RLIM WILD-TYPE" 
D38V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RLIM MUTATED       0                         0     3
  RLIM WILD-TYPE     1                         3    47
D38V12, multiclass
                           clus
vv                          RLIM MUTATED RLIM WILD-TYPE
  ASIAN                                0              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = STK32B MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2               0  1
  STK32B MUTATED    4  0
  STK32B WILD-TYPE 92 18
  STK32B MUTATED STK32B WILD-TYPE 
               4              110 
  STK32B MUTATED STK32B WILD-TYPE 
               0               18 
$`STK32B MUTATED`
TCGA-AF-2693 TCGA-AG-A01Y TCGA-CI-6622 TCGA-DC-6681 
       19.10        64.01         6.97        12.95 

$`STK32B WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        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-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        12.00        70.03        10.98        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         0.49 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05         6.05 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       36.00        10.98        30.05        13.05        10.06         5.29 
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 
        0.49        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 
       37.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  STK32B MUTATED STK32B WILD-TYPE 
            6.97             0.49 
  STK32B MUTATED STK32B WILD-TYPE 
           64.01           126.44 
  STK32B MUTATED STK32B WILD-TYPE 
          16.025           17.260 
[1] "7.0 - 64.0 (16.0)"  "0.5 - 126.4 (17.3)"
[1] "hr="     "2.7e+07"
D39V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  STK32B MUTATED         1        1         0         1         0          0
  STK32B WILD-TYPE      26        6        29         1         5          4
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK32B MUTATED            0          0        0         1
  STK32B WILD-TYPE         15         10       13         5
D39V3, multiclass
            clus
vv           STK32B MUTATED STK32B WILD-TYPE
  STAGE I                 1               26
  STAGE II                1                6
  STAGE IIA               0               29
  STAGE IIB               1                1
  STAGE III               0                5
  STAGE IIIA              0                4
  STAGE IIIB              0               15
  STAGE IIIC              0               10
  STAGE IV                0               13
  STAGE IVA               1                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
  STK32B MUTATED    0  1  2  1
  STK32B WILD-TYPE  8 24 78  8
D39V4, multiclass
    clus
vv   STK32B MUTATED STK32B WILD-TYPE
  T1              0                8
  T2              1               24
  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
  STK32B MUTATED    3  0  1
  STK32B WILD-TYPE 64 32 20
D39V5, multiclass
    clus
vv   STK32B MUTATED STK32B 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"
D39V6, binary
                  cls
clus                0  1
  STK32B MUTATED    2  1
  STK32B WILD-TYPE 90 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK32B MUTATED      2    1
  STK32B WILD-TYPE   90   16
   clus
vv  STK32B MUTATED STK32B WILD-TYPE
  0              2               90
  1              1               16
[1] 2 2
[1] FALSE
D39V7, binary
                  cls
clus                0  1
  STK32B MUTATED    2  2
  STK32B WILD-TYPE 53 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK32B MUTATED      2    2
  STK32B WILD-TYPE   53   65
        clus
vv       STK32B MUTATED STK32B WILD-TYPE
  FEMALE              2               53
  MALE                2               65
[1] 2 2
[1] FALSE
D39V8, binary
                  cls
clus                 0   1
  STK32B MUTATED     3   0
  STK32B WILD-TYPE 103  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK32B MUTATED      3    0
  STK32B WILD-TYPE  103   10
                                clus
vv                               STK32B MUTATED STK32B WILD-TYPE
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 2 2
[1] FALSE
D39V9, binary
                  cls
clus                 0   1
  STK32B MUTATED     0   4
  STK32B WILD-TYPE   4 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK32B MUTATED      0    4
  STK32B WILD-TYPE    4  114
     clus
vv    STK32B MUTATED STK32B WILD-TYPE
  NO               0                4
  YES              4              114
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  STK32B MUTATED    2  0  0  0
  STK32B WILD-TYPE 86  2  9  4
D39V10, multiclass
[1] "Remove cluster labels:" "STK32B MUTATED"        
clus
  STK32B MUTATED STK32B WILD-TYPE 
               2              101 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A020 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6549 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918       TCGA-DC-5337 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157       TCGA-DC-6158 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-DC-6160       TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235 
"STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" "STK32B WILD-TYPE" 
      TCGA-G5-6641 
"STK32B WILD-TYPE" 
D39V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK32B MUTATED       0                         0     3
  STK32B WILD-TYPE     1                         3    47
D39V12, multiclass
                           clus
vv                          STK32B MUTATED STK32B WILD-TYPE
  ASIAN                                  0                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               47
[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"
