[1] "ofn"        "-oTLIHC-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/LIHC-TP/15082975/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15165528/transformed.cor.cli.txt"

nPatients in clinical file=363, in cluster file=198, common to both=194
[1]  18 194
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            61            133 
  TP53 MUTATED TP53 WILD-TYPE 
            61            133 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              50              144 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              50              144 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           15           179 
  RB1 MUTATED RB1 WILD-TYPE 
           15           179 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             185 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             185 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            184 
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            184 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            185 
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            185 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              16              178 
  ARID1A MUTATED ARID1A WILD-TYPE 
              16              178 
[1] "IL6ST MUTATION ANALYSIS"
[1] 3
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             187 
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             187 
[1] "ALB MUTATION ANALYSIS"
[1] 3
  ALB MUTATED ALB WILD-TYPE 
           18           176 
  ALB MUTATED ALB WILD-TYPE 
           18           176 
[1] "HNF1A MUTATION ANALYSIS"
[1] 3
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             186 
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             186 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            23            171 
  APOB MUTATED APOB WILD-TYPE 
            23            171 
[1] "EEF1A1 MUTATION ANALYSIS"
[1] 3
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              189 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              189 
[1] "KIF19 MUTATION ANALYSIS"
[1] 3
  KIF19 MUTATED KIF19 WILD-TYPE 
             10             184 
  KIF19 MUTATED KIF19 WILD-TYPE 
             10             184 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             7            187 
  GNAS MUTATED GNAS WILD-TYPE 
             7            187 
[1] "F5 MUTATION ANALYSIS"
[1] 3
  F5 MUTATED F5 WILD-TYPE 
           4          190 
  F5 MUTATED F5 WILD-TYPE 
           4          190 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            187 
  PTEN MUTATED PTEN WILD-TYPE 
             7            187 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                189 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                189 
[1] "DLK2 MUTATION ANALYSIS"
[1] 3
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            190 
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            190 
[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] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 194 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=73,	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=111,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=16,	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 194 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "RACE"                      "ETHNICITY"                
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
79 50 52 11 
[1] "table(vv)"
vv
T1 T2 T3 T4 
79 50 52 11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
79 50 52 11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
79 50 52 11 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   36 18
  TP53 WILD-TYPE 67 57
  TP53 MUTATED TP53 WILD-TYPE 
            54            124 
  TP53 MUTATED TP53 WILD-TYPE 
            18             57 
$`TP53 MUTATED`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       10.13        27.52        44.42        13.84        22.36        17.98 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       14.60        13.45         0.66         0.07         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EB 
        0.10         0.07         0.10        37.78         2.60        66.31 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A7 
       45.11         6.02        13.64         5.62        25.81        13.78 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-FV-A3I1 
       12.26        13.41         0.20        14.04        13.15         8.12 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        6.38         0.33        81.73         0.39        53.79        28.27 
TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 
       21.53        19.53        22.95        17.10        12.03         1.84 
TCGA-K7-A5RG TCGA-MI-A75G TCGA-MI-A75I TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SK 
       17.06        18.38        20.71         3.09        19.33        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       24.13         0.76        19.76        16.44         1.71         7.04 

$`TP53 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-CC-5259 
        1.12        69.57         5.03         0.26        44.81         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        2.86         3.19         3.39         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH 
       90.71        79.40        19.79        75.65        12.95        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       33.04        18.35        21.14        27.19        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        90.28        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        26.37        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       35.67       114.35        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        9.73         0.20        12.82        13.41        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CH 
        0.03        13.68        51.06        30.74        14.86        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.23        25.25        24.46        20.42         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        5.98         1.02         2.99        37.91        20.75        16.83 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C 
        2.14        11.84        13.38        24.36        12.72         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        12.85         0.62        58.88        17.69        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7ME 
       21.04        19.04        17.59        15.98 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
         81.73         114.35 
  TP53 MUTATED TP53 WILD-TYPE 
        13.710         20.515 
[1] "0.1 - 81.7 (13.7)"  "0.0 - 114.3 (20.5)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED        19       20         0         15          3          0
  TP53 WILD-TYPE      56       24         3         26          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TP53 MUTATED          0         0         0
  TP53 WILD-TYPE        2         1         2
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              19             56
  STAGE II             20             24
  STAGE III             0              3
  STAGE IIIA           15             26
  STAGE IIIB            3              4
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] 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   20 22 18  1
  TP53 WILD-TYPE 59 28 34 10
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           20             59
  T2           22             28
  T3           18             34
  T4            1             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  TP53 MUTATED   35  0
  TP53 WILD-TYPE 87  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     35    0
  TP53 WILD-TYPE   87    3
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           35             87
  1            0              3
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  TP53 MUTATED   46  0
  TP53 WILD-TYPE 96  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     46    0
  TP53 WILD-TYPE   96    4
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           46             96
  1            0              4
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   11 50
  TP53 WILD-TYPE 58 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     11   50
  TP53 WILD-TYPE   58   75
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           11             58
  MALE             50             75
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TP53 MUTATED                         0                       61
  TP53 WILD-TYPE                       1                      129
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TP53 MUTATED                                  0
  TP53 WILD-TYPE                                3
D1V8, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   61            129
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    51   3   0   6
  TP53 WILD-TYPE 108   7   1  11
D1V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           51            108
  R1            3              7
  R2            0              1
  RX            6             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1    22
  TP53 WILD-TYPE                                0    32
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          10    26
  TP53 WILD-TYPE                         4    91
D1V10, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                      22             32
  BLACK OR AFRICAN AMERICAN                  10              4
  WHITE                                      26             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                cls
clus               0   1
  TP53 MUTATED     1  56
  TP53 WILD-TYPE   4 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   56
  TP53 WILD-TYPE    4  118
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           56            118
[1] 2 2
[1] FALSE

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED   29 16
  CTNNB1 WILD-TYPE 74 59
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              45              133 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              16               59 
$`CTNNB1 MUTATED`
TCGA-BC-A10U TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5262 TCGA-DD-A116 TCGA-DD-A119 
       27.52        17.98        14.60         3.39        53.33         7.33 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       51.29        79.40        75.65        33.04        13.64        21.14 
TCGA-DD-A3A4 TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A73A 
       20.12        30.97        26.83        39.78        56.25        23.93 
TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       22.78         1.45         0.20        13.15        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A4ZQ 
       20.61         0.62         9.96        11.93        23.97         0.39 
TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       13.68        21.53        19.53        19.23        22.95        20.42 
TCGA-G3-A6UC TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75H TCGA-O8-A75V 
        7.76        16.83         2.14         9.57        12.85        17.69 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13        16.44         1.71 

$`CTNNB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
        0.26        22.36        44.81        13.45         0.66         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.16         2.86         3.19         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EB 
      113.00         2.60         0.46        21.76        90.71        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       19.79        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG 
       30.61        33.14        32.52        90.28        21.70        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.15        30.51        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
        0.30        80.75        78.84         9.30        23.05        35.67 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      114.35        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB 
        9.73         0.20        12.82        14.04        13.41        19.59 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        60.89        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
        6.38        12.03         0.03         0.33        81.73        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        30.74        14.86        25.64         5.92 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       25.25        24.46        17.10        12.03         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K2 
        1.02         2.99        37.91        20.75        17.06        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.38        24.36        12.72        16.67        18.38        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
        0.62        58.88        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       19.04        15.52         0.76        17.59        19.76        15.98 
TCGA-UB-A7MF 
        7.04 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.20             0.03 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           79.40           114.35 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           19.23            18.35 
[1] "0.2 - 79.4 (19.2)"  "0.0 - 114.3 (18.4)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CTNNB1 MUTATED        21       11         0         11          1          2
  CTNNB1 WILD-TYPE      54       33         3         30          6          4
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CTNNB1 MUTATED          1         1         0
  CTNNB1 WILD-TYPE        1         0         2
D2V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                21               54
  STAGE II               11               33
  STAGE III               0                3
  STAGE IIIA             11               30
  STAGE IIIB              1                6
  STAGE IIIC              2                4
  STAGE IV                1                1
  STAGE IVA               1                0
  STAGE IVB               0                2
[1] 9 2
[1] 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   23 12 13  1
  CTNNB1 WILD-TYPE 56 38 39 10
D2V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1             23               56
  T2             12               38
  T3             13               39
  T4              1               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   30  2
  CTNNB1 WILD-TYPE 92  1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     30    2
  CTNNB1 WILD-TYPE   92    1
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             30               92
  1              2                1
[1] 2 2
[1] FALSE
D2V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    34   1
  CTNNB1 WILD-TYPE 108   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     34    1
  CTNNB1 WILD-TYPE  108    3
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             34              108
  1              1                3
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    6 44
  CTNNB1 WILD-TYPE 63 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6   44
  CTNNB1 WILD-TYPE   63   81
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              6               63
  MALE               44               81
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CTNNB1 MUTATED                         0                       50
  CTNNB1 WILD-TYPE                       1                      140
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CTNNB1 MUTATED                                  0
  CTNNB1 WILD-TYPE                                3
D2V8, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     50              140
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                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"
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    39   4   1   2
  CTNNB1 WILD-TYPE 120   6   0  15
D2V9, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             39              120
  R1              4                6
  R2              1                0
  RX              2               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  1    12
  CTNNB1 WILD-TYPE                                0    42
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           5    31
  CTNNB1 WILD-TYPE                         9    86
D2V10, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                        12               42
  BLACK OR AFRICAN AMERICAN                     5                9
  WHITE                                        31               86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     1  48
  CTNNB1 WILD-TYPE   4 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1   48
  CTNNB1 WILD-TYPE    4  126
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO             48              126
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    7  6
  RB1 WILD-TYPE 96 69
  RB1 MUTATED RB1 WILD-TYPE 
           13           165 
  RB1 MUTATED RB1 WILD-TYPE 
            6            69 
$`RB1 MUTATED`
TCGA-BC-A10W TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A4NE TCGA-DD-A4NJ TCGA-ED-A66Y 
        2.99        79.73        37.78        21.70        30.51         9.73 
TCGA-ED-A7PZ TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-RC-A7S9 
        0.20        53.79        14.86        25.64        25.25        21.04 
TCGA-UB-A7MB 
       19.76 

$`RB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       32.52        90.28        30.97        26.37        30.15        26.83 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       22.78         1.45        35.67       114.35        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       15.85        13.91        13.35         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        30.74        21.53         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        5.98         1.84         1.02         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.72         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
        0.62        58.88        17.69        21.01         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.04        15.52        24.13         0.76        17.59        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        1.71        15.98         7.04 

  RB1 MUTATED RB1 WILD-TYPE 
         0.20          0.03 
  RB1 MUTATED RB1 WILD-TYPE 
        79.73        114.35 
  RB1 MUTATED RB1 WILD-TYPE 
        21.70         17.98 
[1] "0.2 - 79.7 (21.7)"  "0.0 - 114.3 (18.0)"
[1] "hr=" "1.1"
D3V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RB1 MUTATED         3        7         0          4          0          0
  RB1 WILD-TYPE      72       37         3         37          7          6
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  RB1 MUTATED          0         0         0
  RB1 WILD-TYPE        2         1         2
D3V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              3            72
  STAGE II             7            37
  STAGE III            0             3
  STAGE IIIA           4            37
  STAGE IIIB           0             7
  STAGE IIIC           0             6
  STAGE IV             0             2
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  RB1 MUTATED    3  7  4  1
  RB1 WILD-TYPE 76 43 48 10
D3V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           3            76
  T2           7            43
  T3           4            48
  T4           1            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
               cls
clus              0   1
  RB1 MUTATED    11   0
  RB1 WILD-TYPE 111   3
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     11    0
  RB1 WILD-TYPE  111    3
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          11           111
  1           0             3
[1] 2 2
[1] FALSE
D3V6, binary
               cls
clus              0   1
  RB1 MUTATED    13   0
  RB1 WILD-TYPE 129   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13    0
  RB1 WILD-TYPE  129    4
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          13           129
  1           0             4
[1] 2 2
[1] FALSE
D3V7, binary
               cls
clus              0   1
  RB1 MUTATED     7   8
  RB1 WILD-TYPE  62 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      7    8
  RB1 WILD-TYPE   62  117
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           7            62
  MALE             8           117
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RB1 MUTATED                         0                       15
  RB1 WILD-TYPE                       1                      175
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  RB1 MUTATED                                  0
  RB1 WILD-TYPE                                3
D3V8, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  15           175
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             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"
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    14   1   0   0
  RB1 WILD-TYPE 145   9   1  17
D3V9, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          14           145
  R1           1             9
  R2           0             1
  RX           0            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0    10
  RB1 WILD-TYPE                                1    44
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           1     4
  RB1 WILD-TYPE                        13   113
D3V10, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                     10            44
  BLACK OR AFRICAN AMERICAN                  1            13
  WHITE                                      4           113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
               cls
clus              0   1
  RB1 MUTATED     1  14
  RB1 WILD-TYPE   4 160
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   14
  RB1 WILD-TYPE    4  160
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO          14           160
[1] 2 2
[1] FALSE

Clustering(4) Variable = AXIN1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  AXIN1 MUTATED     1   5
  AXIN1 WILD-TYPE 102  70
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              6             172 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              5              70 
$`AXIN1 MUTATED`
TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A39Z TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        0.46        49.15        19.76        22.85        60.89         6.38 

$`AXIN1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        90.28        21.70        30.97        26.37        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        14.40        23.97        19.10        27.88         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.84         1.02         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         2.14        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       16.44         1.71        15.98         7.04 

  AXIN1 MUTATED AXIN1 WILD-TYPE 
           0.46            0.03 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          60.89          114.35 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
         21.305          18.365 
[1] "0.5 - 60.9 (21.3)"  "0.0 - 114.3 (18.4)"
[1] "hr=" "2"  
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AXIN1 MUTATED         3        2         1          1          1          0
  AXIN1 WILD-TYPE      72       42         2         40          6          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  AXIN1 MUTATED          1         0         0
  AXIN1 WILD-TYPE        1         1         2
D4V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I                3              72
  STAGE II               2              42
  STAGE III              1               2
  STAGE IIIA             1              40
  STAGE IIIB             1               6
  STAGE IIIC             0               6
  STAGE IV               1               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] 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
  AXIN1 MUTATED    3  3  2  1
  AXIN1 WILD-TYPE 76 47 50 10
D4V4, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  T1             3              76
  T2             3              47
  T3             2              50
  T4             1              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                 cls
clus                0   1
  AXIN1 MUTATED     6   0
  AXIN1 WILD-TYPE 116   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      6    0
  AXIN1 WILD-TYPE  116    3
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0             6             116
  1             0               3
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus                0   1
  AXIN1 MUTATED     6   1
  AXIN1 WILD-TYPE 136   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      6    1
  AXIN1 WILD-TYPE  136    3
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0             6             136
  1             1               3
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  AXIN1 MUTATED     3   6
  AXIN1 WILD-TYPE  66 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      3    6
  AXIN1 WILD-TYPE   66  119
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             3              66
  MALE               6             119
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AXIN1 MUTATED                         0                        9
  AXIN1 WILD-TYPE                       1                      181
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AXIN1 MUTATED                                  0
  AXIN1 WILD-TYPE                                3
D4V8, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             181
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               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"
                 vv
clus               R0  R1  R2  RX
  AXIN1 MUTATED     7   0   0   2
  AXIN1 WILD-TYPE 152  10   1  15
D4V9, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  R0             7             152
  R1             0              10
  R2             0               1
  RX             2              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN1 MUTATED                                  0     2
  AXIN1 WILD-TYPE                                1    52
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN1 MUTATED                           0     6
  AXIN1 WILD-TYPE                        14   111
D4V10, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              52
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        6             111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                 cls
clus                0   1
  AXIN1 MUTATED     1   7
  AXIN1 WILD-TYPE   4 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      1    7
  AXIN1 WILD-TYPE    4  167
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7             167
[1] 2 2
[1] FALSE

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED    6  4
  BAP1 WILD-TYPE 97 71
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            168 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4             71 
$`BAP1 MUTATED`
TCGA-BC-A10Q TCGA-CC-5260 TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A3A9 TCGA-DD-A4NA 
       37.32         2.86       113.00        12.95        30.61        33.14 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A7PX TCGA-G3-A25T 
      114.35        12.69         0.20        51.06 

$`BAP1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         0.16         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
      107.11        13.78         0.36        32.52        90.28        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        26.37        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
        1.45        35.67        13.41        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73        12.82         0.20        14.04        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        13.68        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       25.25        22.95        24.46        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.03         5.98         1.84         1.02         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06        16.83         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       24.36        12.72         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         0.62        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       21.04        19.33        19.04        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.59        19.76        16.44         1.71        15.98         7.04 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.20           0.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
        114.35         108.76 
  BAP1 MUTATED BAP1 WILD-TYPE 
        31.875         18.365 
[1] "0.2 - 114.3 (31.9)" "0.0 - 108.8 (18.4)"
[1] "hr=" "2"  
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BAP1 MUTATED         2        3         0          1          0          2
  BAP1 WILD-TYPE      73       41         3         40          7          4
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED          0         0         1
  BAP1 WILD-TYPE        2         1         1
D5V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               2             73
  STAGE II              3             41
  STAGE III             0              3
  STAGE IIIA            1             40
  STAGE IIIB            0              7
  STAGE IIIC            2              4
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] 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
  BAP1 MUTATED    2  5  1  2
  BAP1 WILD-TYPE 77 45 51  9
D5V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            2             77
  T2            5             45
  T3            1             51
  T4            2              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"
D5V5, binary
                cls
clus               0   1
  BAP1 MUTATED     7   1
  BAP1 WILD-TYPE 115   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    1
  BAP1 WILD-TYPE  115    2
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            7            115
  1            1              2
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus               0   1
  BAP1 MUTATED     8   1
  BAP1 WILD-TYPE 134   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      8    1
  BAP1 WILD-TYPE  134    3
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            8            134
  1            1              3
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  BAP1 MUTATED     9   1
  BAP1 WILD-TYPE  60 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      9    1
  BAP1 WILD-TYPE   60  124
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            9             60
  MALE              1            124
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BAP1 MUTATED                         0                       10
  BAP1 WILD-TYPE                       1                      180
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BAP1 MUTATED                                  0
  BAP1 WILD-TYPE                                3
D5V8, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   10            180
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED     8   1   0   1
  BAP1 WILD-TYPE 151   9   1  16
D5V9, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0            8            151
  R1            1              9
  R2            0              1
  RX            1             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     3
  BAP1 WILD-TYPE                                1    51
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           0     7
  BAP1 WILD-TYPE                        14   110
D5V10, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3             51
  BLACK OR AFRICAN AMERICAN                   0             14
  WHITE                                       7            110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                cls
clus               0   1
  BAP1 MUTATED     0  10
  BAP1 WILD-TYPE   5 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0   10
  BAP1 WILD-TYPE    5  164
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           10            164
[1] 2 2
[1] FALSE

Clustering(6) Variable = TSC2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  TSC2 MUTATED     3   5
  TSC2 WILD-TYPE 100  70
  TSC2 MUTATED TSC2 WILD-TYPE 
             8            170 
  TSC2 MUTATED TSC2 WILD-TYPE 
             5             70 
$`TSC2 MUTATED`
TCGA-BC-A3KF TCGA-DD-A114 TCGA-DD-A39Z TCGA-DD-A3A6 TCGA-DD-A4NH TCGA-DD-A4NQ 
        0.26        37.78        19.76       107.11        30.15        12.26 
TCGA-G3-A25S TCGA-MI-A75I 
       13.68        20.71 

$`TSC2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
       13.84        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ 
       90.28        21.70        30.97        26.37        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        35.67       114.35        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.15        13.41        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       12.03         0.03         0.33        81.73         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.99        37.91        20.75        17.06        16.83 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C 
        2.14        11.84        13.38        24.36        12.72         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        18.38        12.85         0.62        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  TSC2 MUTATED TSC2 WILD-TYPE 
          0.26           0.03 
  TSC2 MUTATED TSC2 WILD-TYPE 
        107.11         114.35 
  TSC2 MUTATED TSC2 WILD-TYPE 
        20.235         18.365 
[1] "0.3 - 107.1 (20.2)" "0.0 - 114.3 (18.4)"
[1] "hr=" "1.1"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TSC2 MUTATED         2        5         0          0          1          0
  TSC2 WILD-TYPE      73       39         3         41          6          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TSC2 MUTATED          0         0         0
  TSC2 WILD-TYPE        2         1         2
D6V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               2             73
  STAGE II              5             39
  STAGE III             0              3
  STAGE IIIA            0             41
  STAGE IIIB            1              6
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] 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
  TSC2 MUTATED    2  6  1  0
  TSC2 WILD-TYPE 77 44 51 11
D6V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            2             77
  T2            6             44
  T3            1             51
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                cls
clus               0   1
  TSC2 MUTATED     5   0
  TSC2 WILD-TYPE 117   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      5    0
  TSC2 WILD-TYPE  117    3
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            5            117
  1            0              3
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus               0   1
  TSC2 MUTATED     8   0
  TSC2 WILD-TYPE 134   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      8    0
  TSC2 WILD-TYPE  134    4
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            8            134
  1            0              4
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  TSC2 MUTATED     4   5
  TSC2 WILD-TYPE  65 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      4    5
  TSC2 WILD-TYPE   65  120
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  FEMALE            4             65
  MALE              5            120
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TSC2 MUTATED                         0                        9
  TSC2 WILD-TYPE                       1                      181
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TSC2 MUTATED                                  0
  TSC2 WILD-TYPE                                3
D6V8, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    9            181
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  TSC2 MUTATED     8   1   0   0
  TSC2 WILD-TYPE 151   9   1  17
D6V9, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0            8            151
  R1            1              9
  R2            0              1
  RX            0             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC2 MUTATED                                  0     1
  TSC2 WILD-TYPE                                1    53
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC2 MUTATED                           2     5
  TSC2 WILD-TYPE                        12   112
D6V10, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             53
  BLACK OR AFRICAN AMERICAN                   2             12
  WHITE                                       5            112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                cls
clus               0   1
  TSC2 MUTATED     1   6
  TSC2 WILD-TYPE   4 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      1    6
  TSC2 WILD-TYPE    4  168
                        clus
vv                       TSC2 MUTATED TSC2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            6            168
[1] 2 2
[1] FALSE

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    5  8
  ARID1A WILD-TYPE 98 67
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
               8               67 
$`ARID1A MUTATED`
TCGA-CC-5258 TCGA-CC-5262 TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A4NR 
        0.07         3.39        49.15        21.14        27.19         0.30 
TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A23B TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-UB-A7MD 
       19.59        14.40        60.89        24.36        12.72         1.71 
TCGA-UB-A7ME 
       15.98 

$`ARID1A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       13.45         0.66         0.16         2.86         3.19         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        90.28 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        30.97        26.37        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        35.67       114.35        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.15        13.41        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62         9.96        11.93        22.85        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.76        12.03         5.98         1.84         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.91        20.75        17.06        16.83         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        0.62        58.88        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF 
       19.76        16.44         7.04 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.07             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           60.89           114.35 
  ARID1A MUTATED ARID1A WILD-TYPE 
           15.98            18.74 
[1] "0.1 - 60.9 (16.0)"  "0.0 - 114.3 (18.7)"
[1] "hr=" "2"  
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ARID1A MUTATED         7        4         2          2          0          1
  ARID1A WILD-TYPE      68       40         1         39          7          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ARID1A MUTATED          0         0         0
  ARID1A WILD-TYPE        2         1         2
D7V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 7               68
  STAGE II                4               40
  STAGE III               2                1
  STAGE IIIA              2               39
  STAGE IIIB              0                7
  STAGE IIIC              1                5
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] 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    7  4  4  1
  ARID1A WILD-TYPE 72 46 48 10
D7V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              7               72
  T2              4               46
  T3              4               48
  T4              1               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED    10   0
  ARID1A WILD-TYPE 112   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     10    0
  ARID1A WILD-TYPE  112    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             10              112
  1              0                3
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    11   0
  ARID1A WILD-TYPE 131   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     11    0
  ARID1A WILD-TYPE  131    4
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             11              131
  1              0                4
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     6  10
  ARID1A WILD-TYPE  63 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6   10
  ARID1A WILD-TYPE   63  115
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              6               63
  MALE               10              115
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ARID1A MUTATED                         0                       16
  ARID1A WILD-TYPE                       1                      174
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ARID1A MUTATED                                  0
  ARID1A WILD-TYPE                                3
D7V8, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     16              174
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                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"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    12   0   0   3
  ARID1A WILD-TYPE 147  10   1  14
D7V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             12              147
  R1              0               10
  R2              0                1
  RX              3               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     5
  ARID1A WILD-TYPE                                1    49
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2     8
  ARID1A WILD-TYPE                        12   109
D7V10, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         5               49
  BLACK OR AFRICAN AMERICAN                     2               12
  WHITE                                         8              109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  15
  ARID1A WILD-TYPE   5 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   15
  ARID1A WILD-TYPE    5  159
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             15              159
[1] 2 2
[1] FALSE

Clustering(8) Variable = IL6ST MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  IL6ST MUTATED    6  0
  IL6ST WILD-TYPE 97 75
  IL6ST MUTATED IL6ST WILD-TYPE 
              6             172 
  IL6ST MUTATED IL6ST WILD-TYPE 
              0              75 
$`IL6ST MUTATED`
TCGA-DD-A118 TCGA-DD-A1ED TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A459 TCGA-G3-A3CK 
      113.00        75.65        56.25       108.76        13.41        19.23 

$`IL6ST WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.13        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        90.28        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        30.51        39.78        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
       23.05        22.78         1.45        35.67       114.35        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20        14.04        13.15        13.41        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       13.68        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.53        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.84         1.02         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         2.14        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       16.44         1.71        15.98         7.04 

  IL6ST MUTATED IL6ST WILD-TYPE 
          13.41            0.03 
  IL6ST MUTATED IL6ST WILD-TYPE 
         113.00          114.35 
  IL6ST MUTATED IL6ST WILD-TYPE 
         65.950          18.165 
[1] "13.4 - 113.0 (66.0)" "0.0 - 114.3 (18.2)" 
[1] "hr="     "9.1e+07"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IL6ST MUTATED         4        2         0          1          0          0
  IL6ST WILD-TYPE      71       42         3         40          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  IL6ST MUTATED          0         0         0
  IL6ST WILD-TYPE        2         1         2
D8V3, multiclass
            clus
vv           IL6ST MUTATED IL6ST WILD-TYPE
  STAGE I                4              71
  STAGE II               2              42
  STAGE III              0               3
  STAGE IIIA             1              40
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] 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
  IL6ST MUTATED    4  2  1  0
  IL6ST WILD-TYPE 75 48 51 11
D8V4, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  T1             4              75
  T2             2              48
  T3             1              51
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                 cls
clus                0   1
  IL6ST MUTATED     7   0
  IL6ST WILD-TYPE 115   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      7    0
  IL6ST WILD-TYPE  115    3
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             7             115
  1             0               3
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus                0   1
  IL6ST MUTATED     7   0
  IL6ST WILD-TYPE 135   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      7    0
  IL6ST WILD-TYPE  135    4
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             7             135
  1             0               4
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus                0   1
  IL6ST MUTATED     2   5
  IL6ST WILD-TYPE  67 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      2    5
  IL6ST WILD-TYPE   67  120
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  FEMALE             2              67
  MALE               5             120
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  IL6ST MUTATED                         0                        7
  IL6ST WILD-TYPE                       1                      183
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  IL6ST MUTATED                                  0
  IL6ST WILD-TYPE                                3
D8V8, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     7             183
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               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"
                 vv
clus               R0  R1  R2  RX
  IL6ST MUTATED     6   0   0   1
  IL6ST WILD-TYPE 153  10   1  16
D8V9, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  R0             6             153
  R1             0              10
  R2             0               1
  RX             1              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL6ST MUTATED                                  0     3
  IL6ST WILD-TYPE                                1    51
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL6ST MUTATED                           0     4
  IL6ST WILD-TYPE                        14   113
D8V10, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3              51
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        4             113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                 cls
clus                0   1
  IL6ST MUTATED     0   7
  IL6ST WILD-TYPE   5 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      0    7
  IL6ST WILD-TYPE    5  167
                        clus
vv                       IL6ST MUTATED IL6ST WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7             167
[1] 2 2
[1] FALSE

Clustering(9) Variable = ALB MUTATION ANALYSIS
D9V1, survival
               sevent
clus2            0  1
  ALB MUTATED   11  6
  ALB WILD-TYPE 92 69
  ALB MUTATED ALB WILD-TYPE 
           17           161 
  ALB MUTATED ALB WILD-TYPE 
            6            69 
$`ALB MUTATED`
TCGA-BC-4073 TCGA-DD-A1E9 TCGA-DD-A39X TCGA-DD-A4NI TCGA-DD-A4NK TCGA-EP-A26S 
       27.91        90.71        55.69        26.83        39.78        19.99 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-G3-A25S TCGA-G3-A3CJ 
        0.62         9.96        22.85        23.97        13.68        19.53 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-K7-A6G5 TCGA-MI-A75E TCGA-MI-A75G 
       22.95        24.46        16.83        16.67        18.38 

$`ALB WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        27.19         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        90.28        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       22.78         1.45        35.67       114.35        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KA 
        0.20        14.04        13.15        13.41        18.74        20.61 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       19.59        11.93        14.40        60.89        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       21.53        25.64         5.92        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       17.10         7.76        12.03         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.99        37.91        20.75        17.06         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I 
       13.38        24.36        12.72         9.57        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        0.62        58.88        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       19.76        16.44         1.71        15.98         7.04 

  ALB MUTATED ALB WILD-TYPE 
         0.62          0.03 
  ALB MUTATED ALB WILD-TYPE 
        90.71        114.35 
  ALB MUTATED ALB WILD-TYPE 
        22.85         17.69 
[1] "0.6 - 90.7 (22.9)"  "0.0 - 114.3 (17.7)"
[1] "hr=" "1.3"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALB MUTATED        10        3         0          2          1          1
  ALB WILD-TYPE      65       41         3         39          6          5
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  ALB MUTATED          0         1         0
  ALB WILD-TYPE        2         0         2
D9V3, multiclass
            clus
vv           ALB MUTATED ALB WILD-TYPE
  STAGE I             10            65
  STAGE II             3            41
  STAGE III            0             3
  STAGE IIIA           2            39
  STAGE IIIB           1             6
  STAGE IIIC           1             5
  STAGE IV             0             2
  STAGE IVA            1             0
  STAGE IVB            0             2
[1] 9 2
[1] 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
  ALB MUTATED   11  3  2  2
  ALB WILD-TYPE 68 47 50  9
D9V4, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  T1          11            68
  T2           3            47
  T3           2            50
  T4           2             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"
D9V5, binary
               cls
clus              0   1
  ALB MUTATED    10   1
  ALB WILD-TYPE 112   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     10    1
  ALB WILD-TYPE  112    2
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          10           112
  1           1             2
[1] 2 2
[1] FALSE
D9V6, binary
               cls
clus              0   1
  ALB MUTATED    11   0
  ALB WILD-TYPE 131   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     11    0
  ALB WILD-TYPE  131    4
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          11           131
  1           0             4
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  ALB MUTATED     2  16
  ALB WILD-TYPE  67 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      2   16
  ALB WILD-TYPE   67  109
        clus
vv       ALB MUTATED ALB WILD-TYPE
  FEMALE           2            67
  MALE            16           109
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALB MUTATED                         0                       18
  ALB WILD-TYPE                       1                      172
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALB MUTATED                                  0
  ALB WILD-TYPE                                3
D9V8, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  18           172
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             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"
               vv
clus             R0  R1  R2  RX
  ALB MUTATED    13   2   0   1
  ALB WILD-TYPE 146   8   1  16
D9V9, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  R0          13           146
  R1           2             8
  R2           0             1
  RX           1            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALB MUTATED                                  1     1
  ALB WILD-TYPE                                0    53
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALB MUTATED                           1    15
  ALB WILD-TYPE                        13   102
D9V10, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1            53
  BLACK OR AFRICAN AMERICAN                  1            13
  WHITE                                     15           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
               cls
clus              0   1
  ALB MUTATED     0  18
  ALB WILD-TYPE   5 156
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      0   18
  ALB WILD-TYPE    5  156
                        clus
vv                       ALB MUTATED ALB WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          18           156
[1] 2 2
[1] FALSE

Clustering(10) Variable = HNF1A MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  HNF1A MUTATED    5  3
  HNF1A WILD-TYPE 98 72
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             170 
  HNF1A MUTATED HNF1A WILD-TYPE 
              3              72 
$`HNF1A MUTATED`
TCGA-CC-A3M9 TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A39W TCGA-DD-A3A2 TCGA-DD-A73C 
        0.10        21.76        66.31        27.19        70.06        23.05 
TCGA-NI-A4U2 TCGA-T1-A6J8 
       58.88         0.76 

$`HNF1A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        2.60         0.46        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        90.28 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        30.97        26.37        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D 
        0.30        80.75        78.84        23.93         9.30        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        35.67       114.35        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.15        13.41        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.84         1.02         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         2.14        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  HNF1A MUTATED HNF1A WILD-TYPE 
           0.10            0.03 
  HNF1A MUTATED HNF1A WILD-TYPE 
          70.06          114.35 
  HNF1A MUTATED HNF1A WILD-TYPE 
         25.120          18.165 
[1] "0.1 - 70.1 (25.1)"  "0.0 - 114.3 (18.2)"
[1] "hr=" "1.5"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HNF1A MUTATED         3        0         1          3          0          0
  HNF1A WILD-TYPE      72       44         2         38          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  HNF1A MUTATED          0         0         0
  HNF1A WILD-TYPE        2         1         2
D10V3, multiclass
            clus
vv           HNF1A MUTATED HNF1A WILD-TYPE
  STAGE I                3              72
  STAGE II               0              44
  STAGE III              1               2
  STAGE IIIA             3              38
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] 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
  HNF1A MUTATED    4  0  4  0
  HNF1A WILD-TYPE 75 50 48 11
D10V4, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  T1             4              75
  T2             0              50
  T3             4              48
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                 cls
clus                0   1
  HNF1A MUTATED     6   0
  HNF1A WILD-TYPE 116   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      6    0
  HNF1A WILD-TYPE  116    3
   clus
vv  HNF1A MUTATED HNF1A WILD-TYPE
  0             6             116
  1             0               3
[1] 2 2
[1] FALSE
D10V6, binary
                 cls
clus                0   1
  HNF1A MUTATED     7   0
  HNF1A WILD-TYPE 135   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      7    0
  HNF1A WILD-TYPE  135    4
   clus
vv  HNF1A MUTATED HNF1A WILD-TYPE
  0             7             135
  1             0               4
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  HNF1A MUTATED     4   4
  HNF1A WILD-TYPE  65 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      4    4
  HNF1A WILD-TYPE   65  121
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  FEMALE             4              65
  MALE               4             121
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HNF1A MUTATED                         0                        8
  HNF1A WILD-TYPE                       1                      182
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  HNF1A MUTATED                                  0
  HNF1A WILD-TYPE                                3
D10V8, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     8             182
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               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"
                 vv
clus               R0  R1  R2  RX
  HNF1A MUTATED     6   0   0   2
  HNF1A WILD-TYPE 153  10   1  15
D10V9, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  R0             6             153
  R1             0              10
  R2             0               1
  RX             2              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1A MUTATED                                  0     1
  HNF1A WILD-TYPE                                1    53
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1A MUTATED                           0     6
  HNF1A WILD-TYPE                        14   111
D10V10, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              53
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        6             111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                 cls
clus                0   1
  HNF1A MUTATED     0   7
  HNF1A WILD-TYPE   5 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      0    7
  HNF1A WILD-TYPE    5  167
                        clus
vv                       HNF1A MUTATED HNF1A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7             167
[1] 2 2
[1] FALSE

Clustering(11) Variable = APOB MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  APOB MUTATED   11  9
  APOB WILD-TYPE 92 66
  APOB MUTATED APOB WILD-TYPE 
            20            158 
  APOB MUTATED APOB WILD-TYPE 
             9             66 
$`APOB MUTATED`
TCGA-BC-A10Z TCGA-CC-5258 TCGA-CC-5259 TCGA-DD-A1EA TCGA-DD-A1EK TCGA-DD-A3A5 
        1.12         0.07         0.16        79.40        18.35       102.74 
TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NS TCGA-ED-A7XP TCGA-EP-A12J TCGA-G3-A25W 
       13.78        26.37        80.75        13.15        18.74        30.74 
TCGA-G3-A25Y TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A7M6 TCGA-HP-A5MZ TCGA-KR-A7K0 
       14.86         5.92        19.53        12.03         2.99         2.14 
TCGA-RC-A7S9 TCGA-UB-A7MB 
       21.04        19.76 

$`APOB WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 
        7.66        70.06        17.59        20.12       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        90.28        21.70        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A26S 
        0.20        12.82         0.20        14.04        13.41        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH 
       13.68        51.06        53.79        28.27        21.53        25.64 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF 
        7.76         5.98         1.84         1.02        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       58.88        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13         0.76        17.59        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  APOB MUTATED APOB WILD-TYPE 
          0.07           0.03 
  APOB MUTATED APOB WILD-TYPE 
        102.74         114.35 
  APOB MUTATED APOB WILD-TYPE 
        16.605         19.070 
[1] "0.1 - 102.7 (16.6)" "0.0 - 114.3 (19.1)"
[1] "hr=" "1.2"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  APOB MUTATED        10        6         1          2          2          1
  APOB WILD-TYPE      65       38         2         39          5          5
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  APOB MUTATED          0         0         1
  APOB WILD-TYPE        2         1         1
D11V3, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I              10             65
  STAGE II              6             38
  STAGE III             1              2
  STAGE IIIA            2             39
  STAGE IIIB            2              5
  STAGE IIIC            1              5
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] 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
  APOB MUTATED   10  6  5  2
  APOB WILD-TYPE 69 44 47  9
D11V4, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1           10             69
  T2            6             44
  T3            5             47
  T4            2              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"
D11V5, binary
                cls
clus               0   1
  APOB MUTATED    17   0
  APOB WILD-TYPE 105   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     17    0
  APOB WILD-TYPE  105    3
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           17            105
  1            0              3
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus               0   1
  APOB MUTATED    17   1
  APOB WILD-TYPE 125   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     17    1
  APOB WILD-TYPE  125    3
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           17            125
  1            1              3
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  APOB MUTATED    10  13
  APOB WILD-TYPE  59 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     10   13
  APOB WILD-TYPE   59  112
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE           10             59
  MALE             13            112
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  APOB MUTATED                         0                       23
  APOB WILD-TYPE                       1                      167
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  APOB MUTATED                                  0
  APOB WILD-TYPE                                3
D11V8, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   23            167
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  APOB MUTATED    21   0   0   2
  APOB WILD-TYPE 138  10   1  15
D11V9, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           21            138
  R1            0             10
  R2            0              1
  RX            2             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOB MUTATED                                  1     9
  APOB WILD-TYPE                                0    45
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED                           1    10
  APOB WILD-TYPE                        13   107
D11V10, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       9             45
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                      10            107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                cls
clus               0   1
  APOB MUTATED     0  20
  APOB WILD-TYPE   5 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      0   20
  APOB WILD-TYPE    5  154
                        clus
vv                       APOB MUTATED APOB WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           20            154
[1] 2 2
[1] FALSE

Clustering(12) Variable = EEF1A1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  EEF1A1 MUTATED     2   3
  EEF1A1 WILD-TYPE 101  72
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              173 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               3               72 
$`EEF1A1 MUTATED`
TCGA-DD-A11B TCGA-G3-A25V TCGA-G3-A5SM TCGA-KR-A7K0 TCGA-UB-A7MD 
        0.46        28.27        17.10         2.14         1.71 

$`EEF1A1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        90.28        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       26.37        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       35.67       114.35        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        30.74        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.76        12.03         5.98         1.84         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 
       37.91        20.75        17.06        16.83        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       24.36        12.72         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         0.62        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       21.04        19.33        19.04        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       17.59        19.76        16.44        15.98         7.04 

  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
            0.46             0.03 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           28.27           114.35 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
            2.14            19.04 
[1] "0.5 - 28.3 (2.1)"   "0.0 - 114.3 (19.0)"
[1] "hr=" "3.4"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EEF1A1 MUTATED         4        1         0          0          0          0
  EEF1A1 WILD-TYPE      71       43         3         41          7          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  EEF1A1 MUTATED          0         0         0
  EEF1A1 WILD-TYPE        2         1         2
D12V3, multiclass
            clus
vv           EEF1A1 MUTATED EEF1A1 WILD-TYPE
  STAGE I                 4               71
  STAGE II                1               43
  STAGE III               0                3
  STAGE IIIA              0               41
  STAGE IIIB              0                7
  STAGE IIIC              0                6
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] 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
  EEF1A1 MUTATED    4  1  0  0
  EEF1A1 WILD-TYPE 75 49 52 11
D12V4, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  T1              4               75
  T2              1               49
  T3              0               52
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     4   0
  EEF1A1 WILD-TYPE 118   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      4    0
  EEF1A1 WILD-TYPE  118    3
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              4              118
  1              0                3
[1] 2 2
[1] FALSE
D12V6, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     4   0
  EEF1A1 WILD-TYPE 138   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      4    0
  EEF1A1 WILD-TYPE  138    4
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              4              138
  1              0                4
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     0   5
  EEF1A1 WILD-TYPE  69 120
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      0    5
  EEF1A1 WILD-TYPE   69  120
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FEMALE              0               69
  MALE                5              120
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  EEF1A1 MUTATED                         0                        5
  EEF1A1 WILD-TYPE                       1                      185
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  EEF1A1 MUTATED                                  0
  EEF1A1 WILD-TYPE                                3
D12V8, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      5              185
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                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"
                  vv
clus                R0  R1  R2  RX
  EEF1A1 MUTATED     4   0   0   1
  EEF1A1 WILD-TYPE 155  10   1  16
D12V9, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  R0              4              155
  R1              0               10
  R2              0                1
  RX              1               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1A1 MUTATED                                  0     0
  EEF1A1 WILD-TYPE                                1    54
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EEF1A1 MUTATED                           1     4
  EEF1A1 WILD-TYPE                        13   113
D12V10, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               54
  BLACK OR AFRICAN AMERICAN                     1               13
  WHITE                                         4              113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     0   4
  EEF1A1 WILD-TYPE   5 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      0    4
  EEF1A1 WILD-TYPE    5  170
                        clus
vv                       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              170
[1] 2 2
[1] FALSE

Clustering(13) Variable = KIF19 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  KIF19 MUTATED    4  5
  KIF19 WILD-TYPE 99 70
  KIF19 MUTATED KIF19 WILD-TYPE 
              9             169 
  KIF19 MUTATED KIF19 WILD-TYPE 
              5              70 
$`KIF19 MUTATED`
TCGA-BC-A10W TCGA-BC-A10Z TCGA-CC-5263 TCGA-DD-A3A0 TCGA-DD-A4NI TCGA-ED-A459 
        2.99         1.12         4.24        25.81        26.83        13.41 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-UB-A7MB 
       18.74        20.61        19.76 

$`KIF19 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        17.98        14.60        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.07         0.16         2.86         3.19         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       90.28        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       22.78         1.45        35.67       114.35        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
       14.04        13.15        13.41        19.99        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       17.10         7.76        12.03         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.99        37.91        20.75        17.06        16.83         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36        12.72         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71         0.62        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       24.13         0.76        17.59        16.44         1.71        15.98 
TCGA-UB-A7MF 
        7.04 

  KIF19 MUTATED KIF19 WILD-TYPE 
           1.12            0.03 
  KIF19 MUTATED KIF19 WILD-TYPE 
          26.83          114.35 
  KIF19 MUTATED KIF19 WILD-TYPE 
          18.74           18.38 
[1] "1.1 - 26.8 (18.7)"  "0.0 - 114.3 (18.4)"
[1] "hr=" "2.3"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KIF19 MUTATED         3        3         0          3          0          0
  KIF19 WILD-TYPE      72       41         3         38          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KIF19 MUTATED          0         0         0
  KIF19 WILD-TYPE        2         1         2
D13V3, multiclass
            clus
vv           KIF19 MUTATED KIF19 WILD-TYPE
  STAGE I                3              72
  STAGE II               3              41
  STAGE III              0               3
  STAGE IIIA             3              38
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] 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
  KIF19 MUTATED    3  3  3  1
  KIF19 WILD-TYPE 76 47 49 10
D13V4, multiclass
    clus
vv   KIF19 MUTATED KIF19 WILD-TYPE
  T1             3              76
  T2             3              47
  T3             3              49
  T4             1              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                 cls
clus                0   1
  KIF19 MUTATED     4   0
  KIF19 WILD-TYPE 118   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      4    0
  KIF19 WILD-TYPE  118    3
   clus
vv  KIF19 MUTATED KIF19 WILD-TYPE
  0             4             118
  1             0               3
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus                0   1
  KIF19 MUTATED     5   0
  KIF19 WILD-TYPE 137   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      5    0
  KIF19 WILD-TYPE  137    4
   clus
vv  KIF19 MUTATED KIF19 WILD-TYPE
  0             5             137
  1             0               4
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  KIF19 MUTATED     2   8
  KIF19 WILD-TYPE  67 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      2    8
  KIF19 WILD-TYPE   67  117
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  FEMALE             2              67
  MALE               8             117
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KIF19 MUTATED                         0                       10
  KIF19 WILD-TYPE                       1                      180
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KIF19 MUTATED                                  0
  KIF19 WILD-TYPE                                3
D13V8, multiclass
                                  clus
vv                                 KIF19 MUTATED KIF19 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    10             180
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               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"
                 vv
clus               R0  R1  R2  RX
  KIF19 MUTATED     8   1   0   1
  KIF19 WILD-TYPE 151   9   1  16
D13V9, multiclass
    clus
vv   KIF19 MUTATED KIF19 WILD-TYPE
  R0             8             151
  R1             1               9
  R2             0               1
  RX             1              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF19 MUTATED                                  0     4
  KIF19 WILD-TYPE                                1    50
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF19 MUTATED                           1     5
  KIF19 WILD-TYPE                        13   112
D13V10, multiclass
                                  clus
vv                                 KIF19 MUTATED KIF19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4              50
  BLACK OR AFRICAN AMERICAN                    1              13
  WHITE                                        5             112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                 cls
clus                0   1
  KIF19 MUTATED     0  10
  KIF19 WILD-TYPE   5 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      0   10
  KIF19 WILD-TYPE    5  164
                        clus
vv                       KIF19 MUTATED KIF19 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            10             164
[1] 2 2
[1] FALSE

Clustering(14) Variable = GNAS MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    5  1
  GNAS WILD-TYPE 98 74
  GNAS MUTATED GNAS WILD-TYPE 
             6            172 
  GNAS MUTATED GNAS WILD-TYPE 
             1             74 
$`GNAS MUTATED`
TCGA-DD-A118 TCGA-FV-A3R3 TCGA-G3-A25V TCGA-G3-A7M7 TCGA-K7-A5RF TCGA-MI-A75G 
      113.00        12.03        28.27         5.98        20.75        18.38 

$`GNAS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.13        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        90.28        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       26.37        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       35.67       114.35        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 
       23.97        19.10        27.88         8.12         6.38         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        51.06        53.79 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
        7.76        12.03         1.84         1.02         2.99        37.91 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.72         9.57        16.67        12.85        20.71         0.62 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       16.44         1.71        15.98         7.04 

  GNAS MUTATED GNAS WILD-TYPE 
          5.98           0.03 
  GNAS MUTATED GNAS WILD-TYPE 
        113.00         114.35 
  GNAS MUTATED GNAS WILD-TYPE 
        19.565         18.545 
[1] "6.0 - 113.0 (19.6)" "0.0 - 114.3 (18.5)"
[1] "hr=" "3.8"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GNAS MUTATED         4        3         0          0          0          0
  GNAS WILD-TYPE      71       41         3         41          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  GNAS MUTATED          0         0         0
  GNAS WILD-TYPE        2         1         2
D14V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               4             71
  STAGE II              3             41
  STAGE III             0              3
  STAGE IIIA            0             41
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] 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
  GNAS MUTATED    4  3  0  0
  GNAS WILD-TYPE 75 47 52 11
D14V4, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            4             75
  T2            3             47
  T3            0             52
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                cls
clus               0   1
  GNAS MUTATED     4   0
  GNAS WILD-TYPE 118   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      4    0
  GNAS WILD-TYPE  118    3
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            4            118
  1            0              3
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus               0   1
  GNAS MUTATED     4   0
  GNAS WILD-TYPE 138   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      4    0
  GNAS WILD-TYPE  138    4
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            4            138
  1            0              4
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  GNAS MUTATED     2   5
  GNAS WILD-TYPE  67 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      2    5
  GNAS WILD-TYPE   67  120
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            2             67
  MALE              5            120
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GNAS MUTATED                         0                        7
  GNAS WILD-TYPE                       1                      183
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  GNAS MUTATED                                  0
  GNAS WILD-TYPE                                3
D14V8, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    7            183
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  GNAS MUTATED     7   0   0   0
  GNAS WILD-TYPE 152  10   1  17
D14V9, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            7            152
  R1            0             10
  R2            0              1
  RX            0             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNAS MUTATED                                  0     1
  GNAS WILD-TYPE                                1    53
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED                           0     6
  GNAS WILD-TYPE                        14   111
D14V10, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             53
  BLACK OR AFRICAN AMERICAN                   0             14
  WHITE                                       6            111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                cls
clus               0   1
  GNAS MUTATED     0   7
  GNAS WILD-TYPE   5 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0    7
  GNAS WILD-TYPE    5  167
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7            167
[1] 2 2
[1] FALSE

Clustering(15) Variable = F5 MUTATION ANALYSIS
D15V1, survival
              sevent
clus2            0   1
  F5 MUTATED     2   2
  F5 WILD-TYPE 101  73
  F5 MUTATED F5 WILD-TYPE 
           4          174 
  F5 MUTATED F5 WILD-TYPE 
           2           73 
$`F5 MUTATED`
TCGA-ED-A459 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-UB-A7MB 
       13.41        19.59        22.85        19.76 

$`F5 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        90.28        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        26.37        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        35.67       114.35        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.15        13.41        18.74        19.99        20.61         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.76        12.03         5.98         1.84         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.91        20.75        17.06        16.83         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       13.38        24.36        12.72         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71         0.62        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        17.59        16.44         1.71        15.98         7.04 

  F5 MUTATED F5 WILD-TYPE 
       13.41         0.03 
  F5 MUTATED F5 WILD-TYPE 
       22.85       114.35 
  F5 MUTATED F5 WILD-TYPE 
      19.675       18.365 
[1] "13.4 - 22.9 (19.7)" "0.0 - 114.3 (18.4)"
[1] "hr=" "1.7"
D15V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  F5 MUTATED         2        2         0          0          0          0
  F5 WILD-TYPE      73       42         3         41          7          6
              vv
clus           STAGE IV STAGE IVA STAGE IVB
  F5 MUTATED          0         0         0
  F5 WILD-TYPE        2         1         2
D15V3, multiclass
            clus
vv           F5 MUTATED F5 WILD-TYPE
  STAGE I             2           73
  STAGE II            2           42
  STAGE III           0            3
  STAGE IIIA          0           41
  STAGE IIIB          0            7
  STAGE IIIC          0            6
  STAGE IV            0            2
  STAGE IVA           0            1
  STAGE IVB           0            2
[1] 9 2
[1] 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
  F5 MUTATED    2  2  0  0
  F5 WILD-TYPE 77 48 52 11
D15V4, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  T1          2           77
  T2          2           48
  T3          0           52
  T4          0           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
              cls
clus             0   1
  F5 MUTATED     1   0
  F5 WILD-TYPE 121   3
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      1    0
  F5 WILD-TYPE  121    3
   clus
vv  F5 MUTATED F5 WILD-TYPE
  0          1          121
  1          0            3
[1] 2 2
[1] FALSE
D15V6, binary
              cls
clus             0   1
  F5 MUTATED     1   0
  F5 WILD-TYPE 141   4
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      1    0
  F5 WILD-TYPE  141    4
   clus
vv  F5 MUTATED F5 WILD-TYPE
  0          1          141
  1          0            4
[1] 2 2
[1] FALSE
D15V7, binary
              cls
clus             0   1
  F5 MUTATED     1   3
  F5 WILD-TYPE  68 122
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      1    3
  F5 WILD-TYPE   68  122
        clus
vv       F5 MUTATED F5 WILD-TYPE
  FEMALE          1           68
  MALE            3          122
[1] 2 2
[1] FALSE
              vv
clus           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  F5 MUTATED                         0                        4
  F5 WILD-TYPE                       1                      186
              vv
clus           HEPATOCHOLANGIOCARCINOMA (MIXED)
  F5 MUTATED                                  0
  F5 WILD-TYPE                                3
D15V8, multiclass
                                  clus
vv                                 F5 MUTATED F5 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                   0            1
  HEPATOCELLULAR CARCINOMA                  4          186
  HEPATOCHOLANGIOCARCINOMA (MIXED)          0            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"
              vv
clus            R0  R1  R2  RX
  F5 MUTATED     4   0   0   0
  F5 WILD-TYPE 155  10   1  17
D15V9, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  R0          4          155
  R1          0           10
  R2          0            1
  RX          0           17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F5 MUTATED                                  0     1                         0
  F5 WILD-TYPE                                1    53                        14
              vv
clus           WHITE
  F5 MUTATED       3
  F5 WILD-TYPE   114
D15V10, multiclass
                                  clus
vv                                 F5 MUTATED F5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     1           53
  BLACK OR AFRICAN AMERICAN                 0           14
  WHITE                                     3          114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
              cls
clus             0   1
  F5 MUTATED     0   4
  F5 WILD-TYPE   5 170
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      0    4
  F5 WILD-TYPE    5  170
                        clus
vv                       F5 MUTATED F5 WILD-TYPE
  HISPANIC OR LATINO              0            5
  NOT HISPANIC OR LATINO          4          170
[1] 2 2
[1] FALSE

Clustering(16) Variable = PTEN MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     3   3
  PTEN WILD-TYPE 100  72
  PTEN MUTATED PTEN WILD-TYPE 
             6            172 
  PTEN MUTATED PTEN WILD-TYPE 
             3             72 
$`PTEN MUTATED`
TCGA-BC-A112 TCGA-BD-A2L6 TCGA-DD-A11C TCGA-DD-A3A0 TCGA-DD-A4NE TCGA-QA-A7B7 
        5.03        44.81        21.76        25.81        21.70         3.09 

$`PTEN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36        17.98        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       90.28        30.97        26.37        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       22.78         1.45        35.67       114.35        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20        14.04        13.15        13.41        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       13.68        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        5.98         1.84         1.02         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.72         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB 
        0.62        58.88        17.69        21.01        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       16.44         1.71        15.98         7.04 

  PTEN MUTATED PTEN WILD-TYPE 
          3.09           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         44.81         114.35 
  PTEN MUTATED PTEN WILD-TYPE 
        21.730         18.365 
[1] "3.1 - 44.8 (21.7)"  "0.0 - 114.3 (18.4)"
[1] "hr=" "1.4"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTEN MUTATED         2        1         0          2          0          0
  PTEN WILD-TYPE      73       43         3         39          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PTEN MUTATED          0         0         0
  PTEN WILD-TYPE        2         1         2
D16V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               2             73
  STAGE II              1             43
  STAGE III             0              3
  STAGE IIIA            2             39
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PTEN MUTATED    2  2  3  0
  PTEN WILD-TYPE 77 48 49 11
D16V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            2             77
  T2            2             48
  T3            3             49
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                cls
clus               0   1
  PTEN MUTATED     3   0
  PTEN WILD-TYPE 119   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3    0
  PTEN WILD-TYPE  119    3
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            3            119
  1            0              3
[1] 2 2
[1] FALSE
D16V6, binary
                cls
clus               0   1
  PTEN MUTATED     4   0
  PTEN WILD-TYPE 138   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    0
  PTEN WILD-TYPE  138    4
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            4            138
  1            0              4
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus               0   1
  PTEN MUTATED     1   6
  PTEN WILD-TYPE  68 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    6
  PTEN WILD-TYPE   68  119
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            1             68
  MALE              6            119
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PTEN MUTATED                         0                        7
  PTEN WILD-TYPE                       1                      183
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                                3
D16V8, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    7            183
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     5   0   0   2
  PTEN WILD-TYPE 154  10   1  15
D16V9, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            5            154
  R1            0             10
  R2            0              1
  RX            2             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     1
  PTEN WILD-TYPE                                1    53
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           1     5
  PTEN WILD-TYPE                        13   112
D16V10, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             53
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                       5            112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                cls
clus               0   1
  PTEN MUTATED     1   5
  PTEN WILD-TYPE   4 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    5
  PTEN WILD-TYPE    4  169
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            5            169
[1] 2 2
[1] FALSE

Clustering(17) Variable = HIST1H1C MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  HIST1H1C MUTATED    5  0
  HIST1H1C WILD-TYPE 98 75
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                173 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 0                 75 
$`HIST1H1C MUTATED`
TCGA-DD-A73D TCGA-G3-A3CJ TCGA-MI-A75E TCGA-MI-A75G TCGA-UB-A7MA 
       22.78        19.53        16.67        18.38        17.59 

$`HIST1H1C WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 
       13.84         0.26        22.36        17.98        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         0.07         0.16         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        90.28        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        26.37        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E 
       80.75        78.84        23.93         9.30        23.05         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       35.67       114.35        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       17.10         7.76        12.03         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.99        37.91        20.75        17.06        16.83         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H 
       11.84        13.38        24.36        12.72         9.57        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         0.62        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       21.04        19.33        19.04        15.52        24.13         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       19.76        16.44         1.71        15.98         7.04 

  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             16.67               0.03 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             22.78             114.35 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             18.38              18.74 
[1] "16.7 - 22.8 (18.4)" "0.0 - 114.3 (18.7)"
[1] "hr="     "9400000"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  HIST1H1C MUTATED         0        4         0          0          0
  HIST1H1C WILD-TYPE      75       40         3         41          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  HIST1H1C MUTATED            1        0         0         0
  HIST1H1C WILD-TYPE          5        2         1         2
D17V3, multiclass
            clus
vv           HIST1H1C MUTATED HIST1H1C WILD-TYPE
  STAGE I                   0                 75
  STAGE II                  4                 40
  STAGE III                 0                  3
  STAGE IIIA                0                 41
  STAGE IIIB                0                  7
  STAGE IIIC                1                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] 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
  HIST1H1C MUTATED    0  4  0  1
  HIST1H1C WILD-TYPE 79 46 52 10
D17V4, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  T1                0                 79
  T2                4                 46
  T3                0                 52
  T4                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 118   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  118    3
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                4                118
  1                0                  3
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 138   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  138    4
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                4                138
  1                0                  4
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     2   3
  HIST1H1C WILD-TYPE  67 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      2    3
  HIST1H1C WILD-TYPE   67  122
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FEMALE                2                 67
  MALE                  3                122
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HIST1H1C MUTATED                         0                        4
  HIST1H1C WILD-TYPE                       1                      186
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  HIST1H1C MUTATED                                  1
  HIST1H1C WILD-TYPE                                2
D17V8, multiclass
                                  clus
vv                                 HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                        4                186
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  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"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1C MUTATED     4   1   0   0
  HIST1H1C WILD-TYPE 155   9   1  17
D17V9, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  R0                4                155
  R1                1                  9
  R2                0                  1
  RX                0                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1C MUTATED                                  1     0
  HIST1H1C WILD-TYPE                                0    54
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1C MUTATED                           0     4
  HIST1H1C WILD-TYPE                        14   113
D17V10, multiclass
                                  clus
vv                                 HIST1H1C MUTATED HIST1H1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                 54
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           4                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     0   5
  HIST1H1C WILD-TYPE   5 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      0    5
  HIST1H1C WILD-TYPE    5  169
                        clus
vv                       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                169
[1] 2 2
[1] FALSE

Clustering(18) Variable = DLK2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  DLK2 MUTATED     0   3
  DLK2 WILD-TYPE 103  72
  DLK2 MUTATED DLK2 WILD-TYPE 
             3            175 
  DLK2 MUTATED DLK2 WILD-TYPE 
             3             72 
$`DLK2 MUTATED`
TCGA-BC-A112 TCGA-DD-A115 TCGA-ES-A2HT 
        5.03        83.57        14.40 

$`DLK2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        17.98        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        90.28        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      114.35        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        22.85        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.76        12.03         5.98         1.84         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.91        20.75        17.06        16.83         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       13.38        24.36        12.72         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71         0.62        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF 
        7.04 

  DLK2 MUTATED DLK2 WILD-TYPE 
          5.03           0.03 
  DLK2 MUTATED DLK2 WILD-TYPE 
         83.57         114.35 
  DLK2 MUTATED DLK2 WILD-TYPE 
         14.40          18.74 
[1] "5.0 - 83.6 (14.4)"  "0.0 - 114.3 (18.7)"
[1] "hr=" "1.7"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DLK2 MUTATED         1        0         0          2          0          0
  DLK2 WILD-TYPE      74       44         3         39          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  DLK2 MUTATED          0         0         0
  DLK2 WILD-TYPE        2         1         2
D18V3, multiclass
            clus
vv           DLK2 MUTATED DLK2 WILD-TYPE
  STAGE I               1             74
  STAGE II              0             44
  STAGE III             0              3
  STAGE IIIA            2             39
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] 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
  DLK2 MUTATED    1  0  3  0
  DLK2 WILD-TYPE 78 50 49 11
D18V4, multiclass
    clus
vv   DLK2 MUTATED DLK2 WILD-TYPE
  T1            1             78
  T2            0             50
  T3            3             49
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                cls
clus               0   1
  DLK2 MUTATED     2   0
  DLK2 WILD-TYPE 120   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      2    0
  DLK2 WILD-TYPE  120    3
   clus
vv  DLK2 MUTATED DLK2 WILD-TYPE
  0            2            120
  1            0              3
[1] 2 2
[1] FALSE
D18V6, binary
                cls
clus               0   1
  DLK2 MUTATED     2   0
  DLK2 WILD-TYPE 140   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      2    0
  DLK2 WILD-TYPE  140    4
   clus
vv  DLK2 MUTATED DLK2 WILD-TYPE
  0            2            140
  1            0              4
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  DLK2 MUTATED     0   4
  DLK2 WILD-TYPE  69 121
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      0    4
  DLK2 WILD-TYPE   69  121
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  FEMALE            0             69
  MALE              4            121
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DLK2 MUTATED                         0                        4
  DLK2 WILD-TYPE                       1                      186
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DLK2 MUTATED                                  0
  DLK2 WILD-TYPE                                3
D18V8, multiclass
                                  clus
vv                                 DLK2 MUTATED DLK2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    4            186
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              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"
                vv
clus              R0  R1  R2  RX
  DLK2 MUTATED     4   0   0   0
  DLK2 WILD-TYPE 155  10   1  17
D18V9, multiclass
    clus
vv   DLK2 MUTATED DLK2 WILD-TYPE
  R0            4            155
  R1            0             10
  R2            0              1
  RX            0             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLK2 MUTATED                                  0     1
  DLK2 WILD-TYPE                                1    53
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLK2 MUTATED                           1     2
  DLK2 WILD-TYPE                        13   115
D18V10, multiclass
                                  clus
vv                                 DLK2 MUTATED DLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             53
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                       2            115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                cls
clus               0   1
  DLK2 MUTATED     0   3
  DLK2 WILD-TYPE   5 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      0    3
  DLK2 WILD-TYPE    5  171
                        clus
vv                       DLK2 MUTATED DLK2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            171
[1] 2 2
[1] FALSE
