[1] "ofn"        "-oTLUSC-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/LUSC-TP/22506957/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/22595691/transformed.cor.cli.txt"

nPatients in clinical file=504, in cluster file=178, common to both=178
[1]  19 178
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           145             33 
  TP53 MUTATED TP53 WILD-TYPE 
           145             33 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            36            142 
  MLL2 MUTATED MLL2 WILD-TYPE 
            36            142 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            172 
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            172 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            154 
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            154 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              165 
[1] "SLC28A1 MUTATION ANALYSIS"
[1] 3
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
[1] "POLR2B MUTATION ANALYSIS"
[1] 3
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              172 
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              172 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             5            173 
  HRAS MUTATED HRAS WILD-TYPE 
             5            173 
[1] "PI16 MUTATION ANALYSIS"
[1] 3
  PI16 MUTATED PI16 WILD-TYPE 
             7            171 
  PI16 MUTATED PI16 WILD-TYPE 
             7            171 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 178 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=83,	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=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=7,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 178 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=37, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 37 115  14  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 37 115  14  12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 37 115  14  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 37 115  14  12 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
116  39  17   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
116  39  17   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
116  39  17   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
116  39  17   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=56, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=40, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, 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   77 65
  TP53 WILD-TYPE 13 20
  TP53 MUTATED TP53 WILD-TYPE 
           142             33 
  TP53 MUTATED TP53 WILD-TYPE 
            65             20 
$`TP53 MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-22-5471 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-43-5668 TCGA-60-2711 
       60.66       129.01       133.74        19.76        18.38        41.42 
TCGA-60-2712 TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
        9.01        32.32        75.75       117.57        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1076 
       36.07        92.42        86.96         2.79        49.94        60.89 
TCGA-21-1077 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       34.78        31.63        41.69        33.93        10.82         7.33 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
        1.74        14.10        27.02        35.08        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       34.75        13.12        19.30        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25         0.79        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      151.27        14.07         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
       81.24         9.07        60.30        50.66        44.75        39.32 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        4.96         4.01         0.43         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 
        3.39       126.58       111.35        68.58        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.71        24.33        60.53        68.38        71.18        55.56 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-46-3767 TCGA-46-3768 
       39.12        33.11        22.98        21.47        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 
       28.96        12.43        18.25        21.90        10.22        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       80.45        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       35.90        23.57        52.67        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        0.99         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
       23.01         2.01        12.00        24.95        25.97        40.01 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-70-6723 TCGA-85-6560 TCGA-85-6561 
       49.05        12.33        41.39        40.24 

$`TP53 WILD-TYPE`
TCGA-18-5595 TCGA-22-5472 TCGA-39-5039 TCGA-43-2578 TCGA-60-2715 TCGA-18-3412 
       27.19        64.93        17.88        22.49        35.34        11.34 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1081 TCGA-22-1002 
      154.32       119.54        46.88        15.58         9.34         4.31 
TCGA-22-4591 TCGA-34-5234 TCGA-34-5241 TCGA-39-5022 TCGA-39-5030 TCGA-43-6647 
       20.48        74.66        16.93        55.20         1.94        24.89 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-60-2709 TCGA-60-2725 TCGA-60-2726 
        5.46        13.32        12.16        49.48        26.83        11.77 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 
       19.00         3.02        19.00        12.03         3.98         1.97 
TCGA-66-2789 TCGA-70-6722 TCGA-85-6175 
        4.04        12.07         9.67 

  TP53 MUTATED TP53 WILD-TYPE 
          0.39           1.94 
  TP53 MUTATED TP53 WILD-TYPE 
        173.82         154.32 
  TP53 MUTATED TP53 WILD-TYPE 
         25.51          16.93 
[1] "0.4 - 173.8 (25.5)" "1.9 - 154.3 (16.9)"
[1] "hr=" "1.7"
D1V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  TP53 MUTATED         22       56        11        22         20          9
  TP53 WILD-TYPE        7       14         2         4          4          2
                vv
clus             STAGE IV
  TP53 MUTATED          3
  TP53 WILD-TYPE        0
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE IA             22              7
  STAGE IB             56             14
  STAGE IIA            11              2
  STAGE IIB            22              4
  STAGE IIIA           20              4
  STAGE IIIB            9              2
  STAGE IV              3              0
[1] 7 2
[1] 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   29 94 10 12
  TP53 WILD-TYPE  8 21  4  0
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           29              8
  T2           94             21
  T3           10              4
  T4           12              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   92 34 15  3
  TP53 WILD-TYPE 24  5  2  2
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           92             24
  N1           34              5
  N2           15              2
  N3            3              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED   135   3
  TP53 WILD-TYPE  30   0
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    135    3
  TP53 WILD-TYPE   30    0
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          135             30
  1            3              0
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    38 107
  TP53 WILD-TYPE   9  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     38  107
  TP53 WILD-TYPE    9   24
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           38              9
  MALE            107             24
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus              0  1
  TP53 MUTATED   97 16
  TP53 WILD-TYPE 23  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     97   16
  TP53 WILD-TYPE   23    4
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            97             23
  YES           16              4
[1] 2 2
[1] FALSE
D1V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  TP53 MUTATED                                       5
  TP53 WILD-TYPE                                     0
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  TP53 MUTATED                                        1
  TP53 WILD-TYPE                                      0
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                           139
  TP53 WILD-TYPE                                                          33
D1V10, multiclass
                                                             clus
vv                                                            TP53 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          139
                                                             clus
vv                                                            TP53 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, continuous
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   120   2   3   6
  TP53 WILD-TYPE  27   0   1   4
D1V13, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          120             27
  R1            2              0
  R2            3              1
  RX            6              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       3                         7    92
  TP53 WILD-TYPE     2                         2    21
D1V14, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                3              2
  BLACK OR AFRICAN AMERICAN            7              2
  WHITE                               92             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                cls
clus              0  1
  TP53 MUTATED    3 80
  TP53 WILD-TYPE  0 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3   80
  TP53 WILD-TYPE    0   21
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                3              0
  NOT HISPANIC OR LATINO           80             21
[1] 2 2
[1] FALSE

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    9 17
  CDKN2A WILD-TYPE 81 68
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              149 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17               68 
$`CDKN2A MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-3411 TCGA-18-3412 TCGA-21-5786 TCGA-21-5787 
        4.47        31.99       117.57        11.34        33.93        10.82 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4599 TCGA-22-5477 TCGA-22-5492 TCGA-33-4538 
       14.10        35.08        38.17        44.25        16.64        97.94 
TCGA-34-2596 TCGA-34-5231 TCGA-37-4135 TCGA-39-5027 TCGA-39-5028 TCGA-43-3394 
        2.63        65.23         6.81       102.18         1.71        39.12 
TCGA-46-3765 TCGA-51-4080 TCGA-60-2698 TCGA-60-2725 TCGA-60-2726 TCGA-66-2786 
       13.32         0.39        10.22        26.83        11.77        25.97 
TCGA-66-2787 TCGA-66-2792 
       40.01        30.02 

$`CDKN2A WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-22-5471 
       12.20       123.19         4.80         6.18        27.19        60.66 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 
       64.93       129.01       133.74        19.76        17.88        22.49 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94       119.54        46.88        60.89        34.78 
TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 
       15.58         9.34        31.63        41.69         7.33         4.31 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 
        1.74        27.02        20.48        24.13        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5480 
       19.30        11.77        63.55        14.63         0.79        71.34 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4547 TCGA-33-4566 
       11.74        30.12        62.86        56.32        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 
      103.53       151.27        14.07        61.61        32.88        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4141 
       39.32         4.96         4.01         0.43         7.82         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        3.39       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33         1.94        60.53        68.38        71.18        55.56 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3766 
       33.11        22.98        24.89        21.47         5.46        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2707 
       29.95        28.96        12.43        18.25        21.90        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 
       80.45        49.48        66.54        56.91        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
       29.85        35.90        23.57        52.67        16.96        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
       12.03         3.98        12.00        24.95         1.97        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        4.04         5.03        10.06        54.08         4.01        49.05 
TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.07        12.33         9.67        41.39        40.24 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.39             0.39 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          117.57           173.82 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           26.40            23.01 
[1] "0.4 - 117.6 (26.4)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.6"
D2V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CDKN2A MUTATED          5        9         2         4          5          1
  CDKN2A WILD-TYPE       24       61        11        22         19         10
                  vv
clus               STAGE IV
  CDKN2A MUTATED          0
  CDKN2A WILD-TYPE        3
D2V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IA                5               24
  STAGE IB                9               61
  STAGE IIA               2               11
  STAGE IIB               4               22
  STAGE IIIA              5               19
  STAGE IIIB              1               10
  STAGE IV                0                3
[1] 7 2
[1] 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
  CDKN2A MUTATED    5 19  0  2
  CDKN2A WILD-TYPE 32 96 14 10
D2V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              5               32
  T2             19               96
  T3              0               14
  T4              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    15   7   4   0
  CDKN2A WILD-TYPE 101  32  13   5
D2V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             15              101
  N1              7               32
  N2              4               13
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    25   0
  CDKN2A WILD-TYPE 140   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     25    0
  CDKN2A WILD-TYPE  140    3
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             25              140
  1              0                3
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     6  20
  CDKN2A WILD-TYPE  41 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      6   20
  CDKN2A WILD-TYPE   41  111
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              6               41
  MALE               20              111
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    20   2
  CDKN2A WILD-TYPE 100  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     20    2
  CDKN2A WILD-TYPE  100   18
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              20              100
  YES              2               18
[1] 2 2
[1] FALSE
D2V9, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CDKN2A MUTATED                                       1
  CDKN2A WILD-TYPE                                     4
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CDKN2A MUTATED                                        0
  CDKN2A WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                            25
  CDKN2A WILD-TYPE                                                         147
D2V10, multiclass
                                                             clus
vv                                                            CDKN2A MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             25
                                                             clus
vv                                                            CDKN2A WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED    23   0   0   2
  CDKN2A WILD-TYPE 124   2   4   8
D2V13, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             23              124
  R1              0                2
  R2              0                4
  RX              2                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       1                         3    16
  CDKN2A WILD-TYPE     4                         6    97
D2V14, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              3                6
  WHITE                                 16               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                  cls
clus                0  1
  CDKN2A MUTATED    1 15
  CDKN2A WILD-TYPE  2 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   15
  CDKN2A WILD-TYPE    2   86
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             15               86
[1] 2 2
[1] FALSE

Clustering(3) Variable = NFE2L2 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED   14 13
  NFE2L2 WILD-TYPE 76 72
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              148 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13               72 
$`NFE2L2 MUTATED`
TCGA-18-3411 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-22-5473 
      117.57        92.15       154.32        49.94        46.88        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5482 TCGA-33-4586 TCGA-34-2596 TCGA-34-2608 
       14.63        44.25        11.74        14.07         2.63        32.88 
TCGA-34-5236 TCGA-34-5240 TCGA-37-4135 TCGA-39-5022 TCGA-46-3765 TCGA-46-3768 
        9.07        50.66         6.81        55.20        13.32         9.83 
TCGA-51-4079 TCGA-51-4081 TCGA-56-5897 TCGA-60-2709 TCGA-66-2766 TCGA-66-2770 
        0.39        29.95        12.43        49.48         1.02        23.01 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2795 
       24.95        40.01         4.01 

$`NFE2L2 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
       32.32        75.75        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-21-1070 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       86.96         2.79       119.54        60.89        34.78        15.58 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
        9.34        31.63        41.69        33.93        10.82         7.33 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        4.31         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
       24.13        38.17        34.75        13.12        19.30        11.77 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        0.79        71.34        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-34-2600 
       97.94        79.53       173.82       103.53       151.27        61.61 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
       65.23        81.24        74.66        60.30        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4141 
       39.32         4.96         4.01         0.43         7.82         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 
        3.39       126.58       111.35        68.58        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
        5.46        12.16        13.02         4.44        10.65        13.91 
TCGA-51-4080 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 
        0.39        28.96        18.25        21.90        10.22        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       80.45        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       35.90        23.57        26.83        11.77        52.67        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       43.10        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
       43.99        21.01        25.05         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
        3.98        12.00         1.97        25.97        22.98         4.04 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-70-6722 
        5.03        30.02        10.06        54.08        49.05        12.07 
TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.33         9.67        41.39        40.24 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.39             0.39 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          154.32           173.82 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           24.95            23.26 
[1] "0.4 - 154.3 (24.9)" "0.4 - 173.8 (23.3)"
[1] "hr=" "1"  
D3V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  NFE2L2 MUTATED          5       10         0         5          4          2
  NFE2L2 WILD-TYPE       24       60        13        21         20          9
                  vv
clus               STAGE IV
  NFE2L2 MUTATED          0
  NFE2L2 WILD-TYPE        3
D3V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE IA                5               24
  STAGE IB               10               60
  STAGE IIA               0               13
  STAGE IIB               5               21
  STAGE IIIA              4               20
  STAGE IIIB              2                9
  STAGE IV                0                3
[1] 7 2
[1] 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
  NFE2L2 MUTATED    5 17  4  1
  NFE2L2 WILD-TYPE 32 98 10 11
D3V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              5               32
  T2             17               98
  T3              4               10
  T4              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NFE2L2 MUTATED   18  5  3  1
  NFE2L2 WILD-TYPE 98 34 14  4
D3V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             18               98
  N1              5               34
  N2              3               14
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    24   0
  NFE2L2 WILD-TYPE 141   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     24    0
  NFE2L2 WILD-TYPE  141    3
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             24              141
  1              0                3
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     4  23
  NFE2L2 WILD-TYPE  43 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4   23
  NFE2L2 WILD-TYPE   43  108
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              4               43
  MALE               23              108
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    18   5
  NFE2L2 WILD-TYPE 102  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     18    5
  NFE2L2 WILD-TYPE  102   15
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              18              102
  YES              5               15
[1] 2 2
[1] FALSE
D3V9, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED                                       1
  NFE2L2 WILD-TYPE                                     4
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  NFE2L2 MUTATED                                        0
  NFE2L2 WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NFE2L2 MUTATED                                                            26
  NFE2L2 WILD-TYPE                                                         146
D3V10, multiclass
                                                             clus
vv                                                            NFE2L2 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             26
                                                             clus
vv                                                            NFE2L2 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, continuous
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    22   0   1   0
  NFE2L2 WILD-TYPE 125   2   3  10
D3V13, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             22              125
  R1              0                2
  R2              1                3
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED       0                         2    17
  NFE2L2 WILD-TYPE     5                         7    96
D3V14, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 17               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    0 16
  NFE2L2 WILD-TYPE  3 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   16
  NFE2L2 WILD-TYPE    3   85
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16               85
[1] 2 2
[1] FALSE

Clustering(4) Variable = MLL2 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   17 19
  MLL2 WILD-TYPE 73 66
  MLL2 MUTATED MLL2 WILD-TYPE 
            36            139 
  MLL2 MUTATED MLL2 WILD-TYPE 
            19             66 
$`MLL2 MUTATED`
TCGA-18-3416 TCGA-18-4083 TCGA-18-3411 TCGA-18-3414 TCGA-21-1078 TCGA-22-1002 
       31.99         6.18       117.57        23.54        15.58         4.31 
TCGA-22-1016 TCGA-22-4599 TCGA-22-5473 TCGA-22-5477 TCGA-22-5482 TCGA-33-4538 
       27.02        38.17        63.55        44.25        11.74        97.94 
TCGA-34-2596 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
        2.63        44.75        39.32         0.43         7.82         6.81 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-43-3394 TCGA-46-3765 
      102.18         1.94        60.53        71.18        39.12        13.32 
TCGA-56-5897 TCGA-56-6545 TCGA-60-2698 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       12.43        21.90        10.22        11.77        52.67        16.96 
TCGA-66-2744 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2773 TCGA-70-6722 
        0.99         2.01         2.01         2.01         3.02        12.07 

$`MLL2 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-22-5471 
       12.20         4.47       123.19         4.80        27.19        60.66 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 
       64.93       129.01       133.74        19.76        17.88        22.49 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       11.34        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94       119.54        46.88        60.89        34.78 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
        9.34        31.63        41.69        33.93        10.82         7.33 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 
        1.74        14.10        20.48        35.08        24.13        34.75 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 TCGA-22-5478 TCGA-22-5480 
       13.12        19.30        11.77        14.63         0.79        71.34 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 
       30.12        62.86        56.32        16.64        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      103.53       151.27        14.07        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5929 TCGA-37-3783 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        4.96         4.01         0.39         3.39       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 
       68.58        55.20        82.52         1.71        24.33        68.38 
TCGA-39-5037 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       55.56        33.11        22.98        24.89        21.47         5.46 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5898 TCGA-60-2707 
        0.39         0.39        29.95        28.96        18.25        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 
       80.45        49.48        66.54        56.91        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-66-2734 TCGA-66-2742 
       29.85        35.90        23.57        26.83        43.10        21.07 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        0.99         1.02        23.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       40.01        22.98         4.04         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
       54.08         4.01        49.05        12.33         9.67        41.39 
TCGA-85-6561 
       40.24 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.43           0.39 
  MLL2 MUTATED MLL2 WILD-TYPE 
        117.57         173.82 
  MLL2 MUTATED MLL2 WILD-TYPE 
         14.45          24.89 
[1] "0.4 - 117.6 (14.4)" "0.4 - 173.8 (24.9)"
[1] "hr=" "1.4"
D4V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  MLL2 MUTATED          6       13         2         7          5          1
  MLL2 WILD-TYPE       23       57        11        19         19         10
                vv
clus             STAGE IV
  MLL2 MUTATED          1
  MLL2 WILD-TYPE        2
D4V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE IA              6             23
  STAGE IB             13             57
  STAGE IIA             2             11
  STAGE IIB             7             19
  STAGE IIIA            5             19
  STAGE IIIB            1             10
  STAGE IV              1              2
[1] 7 2
[1] 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
  MLL2 MUTATED    6 26  2  2
  MLL2 WILD-TYPE 31 89 12 10
D4V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            6             31
  T2           26             89
  T3            2             12
  T4            2             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   22 10  3  1
  MLL2 WILD-TYPE 94 29 14  4
D4V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           22             94
  N1           10             29
  N2            3             14
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                cls
clus               0   1
  MLL2 MUTATED    33   1
  MLL2 WILD-TYPE 132   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     33    1
  MLL2 WILD-TYPE  132    2
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           33            132
  1            1              2
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  MLL2 MUTATED     9  27
  MLL2 WILD-TYPE  38 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      9   27
  MLL2 WILD-TYPE   38  104
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE            9             38
  MALE             27            104
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus              0  1
  MLL2 MUTATED   24  2
  MLL2 WILD-TYPE 96 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     24    2
  MLL2 WILD-TYPE   96   18
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            24             96
  YES            2             18
[1] 2 2
[1] FALSE
D4V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  MLL2 MUTATED                                       0
  MLL2 WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  MLL2 MUTATED                                        0
  MLL2 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                            36
  MLL2 WILD-TYPE                                                         136
D4V10, multiclass
                                                             clus
vv                                                            MLL2 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           36
                                                             clus
vv                                                            MLL2 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    30   0   0   3
  MLL2 WILD-TYPE 117   2   4   7
D4V13, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           30            117
  R1            0              2
  R2            0              4
  RX            3              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       3                         1    22
  MLL2 WILD-TYPE     2                         8    91
D4V14, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                3              2
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                               22             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                cls
clus              0  1
  MLL2 MUTATED    1 17
  MLL2 WILD-TYPE  2 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   17
  MLL2 WILD-TYPE    2   84
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           17             84
[1] 2 2
[1] FALSE

Clustering(5) Variable = KEAP1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  KEAP1 MUTATED   13  9
  KEAP1 WILD-TYPE 77 76
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             153 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
              9              76 
$`KEAP1 MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-33-4532 TCGA-43-2578 TCGA-21-1077 
        4.47       123.19        27.19       129.01        22.49        34.78 
TCGA-22-4599 TCGA-33-4538 TCGA-37-4133 TCGA-37-5819 TCGA-39-5031 TCGA-39-5036 
       38.17        97.94         7.82         3.39        60.53        71.18 
TCGA-43-6143 TCGA-46-6025 TCGA-51-4081 TCGA-60-2710 TCGA-60-2722 TCGA-60-2723 
       22.98        10.65        29.95        66.54        29.85        35.90 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2773 TCGA-66-2777 
        2.01         0.99         3.02         2.01 

$`KEAP1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-22-5472 
       12.20         4.80        31.99         6.18        60.66        64.93 
TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 
      133.74        19.76        17.88        18.38        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       35.34        32.32        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 
       49.94       119.54        46.88        60.89        15.58         9.34 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       31.63        41.69        33.93        10.82         7.33         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
        1.74        14.10        27.02        20.48        35.08        24.13 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       34.75        13.12        19.30        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25         0.79        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       56.32        16.64        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       14.07         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4135 TCGA-37-4141 
       39.32         4.96         4.01         0.43         6.81         0.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 TCGA-39-5037 TCGA-43-3394 
        1.71        24.33         1.94        68.38        55.56        39.12 
TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 
       33.11        24.89        21.47         5.46        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       13.02         9.83         4.44        13.91         0.39         0.39 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 
       28.96        12.43        18.25        21.90        10.22        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 
       80.45        49.48        56.91        42.64         3.19        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       26.83        11.77        52.67        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.99         0.92        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         2.01        23.01        19.00 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
       25.97        40.01        22.98         4.04         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 
       10.06        54.08         4.01        49.05        12.07        12.33 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
        9.67        41.39        40.24 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           0.99            0.39 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         129.01          173.82 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          28.52           23.01 
[1] "1.0 - 129.0 (28.5)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  KEAP1 MUTATED          3        9         1         4          4          1
  KEAP1 WILD-TYPE       26       61        12        22         20         10
                 vv
clus              STAGE IV
  KEAP1 MUTATED          0
  KEAP1 WILD-TYPE        3
D5V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE IA               3              26
  STAGE IB               9              61
  STAGE IIA              1              12
  STAGE IIB              4              22
  STAGE IIIA             4              20
  STAGE IIIB             1              10
  STAGE IV               0               3
[1] 7 2
[1] 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
  KEAP1 MUTATED    4 16  0  2
  KEAP1 WILD-TYPE 33 99 14 10
D5V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1             4              33
  T2            16              99
  T3             0              14
  T4             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KEAP1 MUTATED    14   5   3   0
  KEAP1 WILD-TYPE 102  34  14   5
D5V5, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  N0            14             102
  N1             5              34
  N2             3              14
  N3             0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  KEAP1 MUTATED    22   0
  KEAP1 WILD-TYPE 143   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     22    0
  KEAP1 WILD-TYPE  143    3
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0            22             143
  1             0               3
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED     5  17
  KEAP1 WILD-TYPE  42 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      5   17
  KEAP1 WILD-TYPE   42  114
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             5              42
  MALE              17             114
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED    14   0
  KEAP1 WILD-TYPE 106  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     14    0
  KEAP1 WILD-TYPE  106   20
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO             14             106
  YES             0              20
[1] 2 2
[1] FALSE
D5V9, continuous
                 vv
clus              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  KEAP1 MUTATED                                       2
  KEAP1 WILD-TYPE                                     3
                 vv
clus              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  KEAP1 MUTATED                                        0
  KEAP1 WILD-TYPE                                      1
                 vv
clus              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                            20
  KEAP1 WILD-TYPE                                                         152
D5V10, multiclass
                                                             clus
vv                                                            KEAP1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            20
                                                             clus
vv                                                            KEAP1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                 vv
clus               R0  R1  R2  RX
  KEAP1 MUTATED    19   0   0   2
  KEAP1 WILD-TYPE 128   2   4   8
D5V13, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            19             128
  R1             0               2
  R2             0               4
  RX             2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED       1                         0    15
  KEAP1 WILD-TYPE     4                         9    98
D5V14, multiclass
                           clus
vv                          KEAP1 MUTATED KEAP1 WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               9
  WHITE                                15              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                 cls
clus               0  1
  KEAP1 MUTATED    1 13
  KEAP1 WILD-TYPE  2 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      1   13
  KEAP1 WILD-TYPE    2   88
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            13              88
[1] 2 2
[1] FALSE

Clustering(6) Variable = PTEN MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    7  6
  PTEN WILD-TYPE 83 79
  PTEN MUTATED PTEN WILD-TYPE 
            13            162 
  PTEN MUTATED PTEN WILD-TYPE 
             6             79 
$`PTEN MUTATED`
TCGA-43-2578 TCGA-18-3417 TCGA-18-3421 TCGA-22-4599 TCGA-22-5489 TCGA-33-4583 
       22.49        36.07        86.96        38.17        62.86       151.27 
TCGA-39-5024 TCGA-39-5027 TCGA-43-3920 TCGA-56-5897 TCGA-60-2707 TCGA-66-2783 
       82.52       102.18        33.11        12.43        21.93        24.95 
TCGA-66-2788 
       22.98 

$`PTEN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       17.88        18.38        41.42         9.01        35.34        32.32 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
       75.75       117.57        11.34        23.54        92.15        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        2.79       154.32        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       34.78        15.58         9.34        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
       20.48        35.08        24.13        34.75        13.12        19.30 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
       11.77        63.55        14.63        44.25         0.79        71.34 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       11.74        30.12        56.32        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      173.82       103.53        14.07         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 
       16.93        44.75        39.32         4.96         4.01         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         0.39         3.39       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       68.58        55.20         1.71        24.33         1.94        60.53 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 
       68.38        71.18        55.56        39.12        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       21.47         5.46        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2708 TCGA-60-2709 
       28.96        18.25        21.90        10.22        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       66.54        56.91        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
       23.57        26.83        11.77        52.67        16.96        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03         3.98        12.00         1.97        25.97        40.01 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       49.05        12.07        12.33         9.67        41.39        40.24 

  PTEN MUTATED PTEN WILD-TYPE 
         12.43           0.39 
  PTEN MUTATED PTEN WILD-TYPE 
        151.27         173.82 
  PTEN MUTATED PTEN WILD-TYPE 
         36.07          22.44 
[1] "12.4 - 151.3 (36.1)" "0.4 - 173.8 (22.4)" 
[1] "hr=" "1.7"
D6V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  PTEN MUTATED          4        6         1         0          1          1
  PTEN WILD-TYPE       25       64        12        26         23         10
                vv
clus             STAGE IV
  PTEN MUTATED          1
  PTEN WILD-TYPE        2
D6V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE IA              4             25
  STAGE IB              6             64
  STAGE IIA             1             12
  STAGE IIB             0             26
  STAGE IIIA            1             23
  STAGE IIIB            1             10
  STAGE IV              1              2
[1] 7 2
[1] 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     4  10   0   0
  PTEN WILD-TYPE  33 105  14  12
D6V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            4             33
  T2           10            105
  T3            0             14
  T4            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED    11   1   1   1
  PTEN WILD-TYPE 105  38  16   4
D6V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           11            105
  N1            1             38
  N2            1             16
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                cls
clus               0   1
  PTEN MUTATED    11   1
  PTEN WILD-TYPE 154   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     11    1
  PTEN WILD-TYPE  154    2
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           11            154
  1            1              2
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  PTEN MUTATED     3  11
  PTEN WILD-TYPE  44 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3   11
  PTEN WILD-TYPE   44  120
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            3             44
  MALE             11            120
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  PTEN MUTATED    12   1
  PTEN WILD-TYPE 108  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     12    1
  PTEN WILD-TYPE  108   19
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            12            108
  YES            1             19
[1] 2 2
[1] FALSE
D6V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  PTEN MUTATED                                       0
  PTEN WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  PTEN MUTATED                                        0
  PTEN WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                            14
  PTEN WILD-TYPE                                                         158
D6V10, multiclass
                                                             clus
vv                                                            PTEN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           14
                                                             clus
vv                                                            PTEN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    10   0   1   1
  PTEN WILD-TYPE 137   2   3   9
D6V13, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           10            137
  R1            0              2
  R2            1              3
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0    10
  PTEN WILD-TYPE     5                         9   103
D6V14, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                               10            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                cls
clus              0  1
  PTEN MUTATED    1  8
  PTEN WILD-TYPE  2 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    8
  PTEN WILD-TYPE    2   93
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            8             93
[1] 2 2
[1] FALSE

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   12 15
  PIK3CA WILD-TYPE 78 70
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              148 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15               70 
$`PIK3CA MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-5595 TCGA-18-3414 TCGA-21-1071 TCGA-21-1078 
        4.47         4.80        27.19        23.54        46.88        15.58 
TCGA-21-5782 TCGA-22-4613 TCGA-22-5473 TCGA-22-5489 TCGA-22-5491 TCGA-33-4547 
       31.63        11.77        63.55        62.86        56.32        79.53 
TCGA-33-4583 TCGA-34-5232 TCGA-37-3783 TCGA-37-5819 TCGA-46-3767 TCGA-51-4079 
      151.27        81.24         4.01         3.39        13.02         0.39 
TCGA-60-2724 TCGA-60-2726 TCGA-66-2755 TCGA-66-2759 TCGA-66-2766 TCGA-66-2773 
       23.57        11.77         0.92        25.05         1.02         3.02 
TCGA-66-2785 TCGA-70-6722 TCGA-85-6560 
        1.97        12.07        41.39 

$`PIK3CA WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-22-5472 
       12.20       123.19        31.99         6.18        60.66        64.93 
TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
      129.01       133.74        19.76        17.88        22.49        18.38 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 
       41.42         9.01        35.34        32.32        75.75       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       11.34        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 
      154.32        49.94       119.54        60.89        34.78         9.34 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
       41.69        33.93        10.82         7.33         4.31         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
       14.10        27.02        20.48        35.08        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       34.75        13.12        19.30        14.63        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 
       71.34        11.74        30.12        16.64        97.94       173.82 
TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      103.53        14.07         2.63        61.61        32.88        65.23 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
       39.32         4.96         0.43         7.82         6.81         0.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
        5.46        13.32        12.16         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       13.91         0.39        29.95        28.96        12.43        18.25 
TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       21.90        10.22        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       56.91        42.64         3.19        29.85        35.90        26.83 
TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       52.67        16.96        43.10        21.07         0.99         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99        43.99        21.01         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        23.01        19.00         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        12.00        24.95        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-70-6723 TCGA-85-6175 TCGA-85-6561 
       49.05        12.33         9.67        40.24 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.39             0.39 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          151.27           173.82 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           15.58            24.23 
[1] "0.4 - 151.3 (15.6)" "0.4 - 173.8 (24.2)"
[1] "hr=" "1.4"
D7V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  PIK3CA MUTATED          5       10         3         1          6          0
  PIK3CA WILD-TYPE       24       60        10        25         18         11
                  vv
clus               STAGE IV
  PIK3CA MUTATED          1
  PIK3CA WILD-TYPE        2
D7V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE IA                5               24
  STAGE IB               10               60
  STAGE IIA               3               10
  STAGE IIB               1               25
  STAGE IIIA              6               18
  STAGE IIIB              0               11
  STAGE IV                1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     7  14   5   1
  PIK3CA WILD-TYPE  30 101   9  11
D7V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              7               30
  T2             14              101
  T3              5                9
  T4              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   17  6  4  0
  PIK3CA WILD-TYPE 99 33 13  5
D7V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             17               99
  N1              6               33
  N2              4               13
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    25   1
  PIK3CA WILD-TYPE 140   2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     25    1
  PIK3CA WILD-TYPE  140    2
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             25              140
  1              1                2
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     4  23
  PIK3CA WILD-TYPE  43 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      4   23
  PIK3CA WILD-TYPE   43  108
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              4               43
  MALE               23              108
[1] 2 2
[1] FALSE
D7V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    16   2
  PIK3CA WILD-TYPE 104  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     16    2
  PIK3CA WILD-TYPE  104   18
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              16              104
  YES              2               18
[1] 2 2
[1] FALSE
D7V9, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED                                       0
  PIK3CA WILD-TYPE                                     5
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  PIK3CA MUTATED                                        0
  PIK3CA WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                            27
  PIK3CA WILD-TYPE                                                         145
D7V10, multiclass
                                                             clus
vv                                                            PIK3CA MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             27
                                                             clus
vv                                                            PIK3CA WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    25   0   0   1
  PIK3CA WILD-TYPE 122   2   4   9
D7V13, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             25              122
  R1              0                2
  R2              0                4
  RX              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       3                         2    15
  PIK3CA WILD-TYPE     2                         7    98
D7V14, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  3                2
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 15               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                  cls
clus                0  1
  PIK3CA MUTATED    0 17
  PIK3CA WILD-TYPE  3 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   17
  PIK3CA WILD-TYPE    3   84
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             17               84
[1] 2 2
[1] FALSE

Clustering(8) Variable = RB1 MUTATION ANALYSIS
D8V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    5  7
  RB1 WILD-TYPE 85 78
  RB1 MUTATED RB1 WILD-TYPE 
           12           163 
  RB1 MUTATED RB1 WILD-TYPE 
            7            78 
$`RB1 MUTATED`
TCGA-33-4533 TCGA-43-2578 TCGA-18-4086 TCGA-22-4601 TCGA-22-4607 TCGA-34-5240 
      133.74        22.49         2.79        34.75        19.30        50.66 
TCGA-39-5021 TCGA-39-5031 TCGA-43-6143 TCGA-56-1622 TCGA-66-2754 TCGA-66-2783 
       68.58        60.53        22.98        28.96         2.01        24.95 

$`RB1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-6737 TCGA-39-5039 
       27.19        60.66        64.93       129.01        19.76        17.88 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
       86.96       154.32        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       34.78        15.58         9.34        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 
       20.48        35.08        24.13        38.17        13.12        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
       63.55        14.63        44.25         0.79        71.34        11.74 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       30.12        62.86        56.32        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 
      173.82       103.53       151.27        14.07         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 
       16.93        44.75        39.32         4.96         4.01         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         0.39         3.39       126.58       111.35 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        82.52       102.18         1.71        24.33         1.94 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 
       68.38        71.18        55.56        39.12        33.11        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       21.47         5.46        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       12.43        18.25        21.90        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       35.90        23.57        26.83        11.77        52.67        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       43.10        21.07         0.99         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03         3.98        12.00         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
        4.01        49.05        12.07        12.33         9.67        41.39 
TCGA-85-6561 
       40.24 

  RB1 MUTATED RB1 WILD-TYPE 
         2.01          0.39 
  RB1 MUTATED RB1 WILD-TYPE 
       133.74        173.82 
  RB1 MUTATED RB1 WILD-TYPE 
       26.955        23.010 
[1] "2.0 - 133.7 (27.0)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.1"
D8V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  RB1 MUTATED          2        6         0         1          2          1
  RB1 WILD-TYPE       27       64        13        25         22         10
               vv
clus            STAGE IV
  RB1 MUTATED          0
  RB1 WILD-TYPE        3
D8V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE IA             2            27
  STAGE IB             6            64
  STAGE IIA            0            13
  STAGE IIB            1            25
  STAGE IIIA           2            22
  STAGE IIIB           1            10
  STAGE IV             0             3
[1] 7 2
[1] 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     2   9   0   1
  RB1 WILD-TYPE  35 106  14  11
D8V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           2            35
  T2           9           106
  T3           0            14
  T4           1            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RB1 MUTATED     9   1   1   1
  RB1 WILD-TYPE 107  38  16   4
D8V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           9           107
  N1           1            38
  N2           1            16
  N3           1             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
               cls
clus              0   1
  RB1 MUTATED    12   0
  RB1 WILD-TYPE 153   3
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     12    0
  RB1 WILD-TYPE  153    3
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          12           153
  1           0             3
[1] 2 2
[1] FALSE
D8V7, binary
               cls
clus              0   1
  RB1 MUTATED     5   7
  RB1 WILD-TYPE  42 124
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5    7
  RB1 WILD-TYPE   42  124
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           5            42
  MALE             7           124
[1] 2 2
[1] FALSE
D8V8, binary
               cls
clus              0   1
  RB1 MUTATED     8   1
  RB1 WILD-TYPE 112  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      8    1
  RB1 WILD-TYPE  112   19
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            8           112
  YES           1            19
[1] 2 2
[1] FALSE
D8V9, continuous
               vv
clus            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  RB1 MUTATED                                       2
  RB1 WILD-TYPE                                     3
               vv
clus            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  RB1 MUTATED                                        0
  RB1 WILD-TYPE                                      1
               vv
clus            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RB1 MUTATED                                                            10
  RB1 WILD-TYPE                                                         162
D8V10, multiclass
                                                             clus
vv                                                            RB1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          10
                                                             clus
vv                                                            RB1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED     9   0   1   1
  RB1 WILD-TYPE 138   2   3   9
D8V13, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0           9           138
  R1           0             2
  R2           1             3
  RX           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         1     7
  RB1 WILD-TYPE     5                         8   106
D8V14, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           1             8
  WHITE                               7           106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
               cls
clus             0  1
  RB1 MUTATED    0  6
  RB1 WILD-TYPE  3 95
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    6
  RB1 WILD-TYPE    3   95
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           6            95
[1] 2 2
[1] FALSE

Clustering(9) Variable = CYP11B1 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  CYP11B1 MUTATED    4 11
  CYP11B1 WILD-TYPE 86 74
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               160 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               11                74 
$`CYP11B1 MUTATED`
TCGA-21-1077 TCGA-21-5787 TCGA-22-1016 TCGA-22-4595 TCGA-22-5491 TCGA-33-4566 
       34.78        10.82        27.02        24.13        56.32       173.82 
TCGA-43-6771 TCGA-51-4079 TCGA-51-4080 TCGA-60-2719 TCGA-60-2726 TCGA-66-2766 
        5.46         0.39         0.39        42.64        11.77         1.02 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2789 
       24.95         1.97         4.04 

$`CYP11B1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
      119.54        46.88        60.89        15.58         9.34        31.63 
TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       41.69        33.93         7.33         4.31         1.74        14.10 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
       20.48        35.08        38.17        34.75        13.12        19.30 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
       11.77        63.55        14.63        44.25         0.79        71.34 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       11.74        30.12        62.86        16.64        97.94        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      103.53       151.27        14.07         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 
       16.93        44.75        39.32         4.96         4.01         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         0.39         3.39       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 
        1.94        60.53        68.38        71.18        55.56        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-46-3765 TCGA-46-3766 
       33.11        22.98        24.89        21.47        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 
       13.02         9.83         4.44        10.65        13.91        29.95 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 
       28.96        12.43        18.25        21.90        10.22        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2720 TCGA-60-2722 
       80.45        49.48        66.54        56.91         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
       35.90        23.57        26.83        52.67        16.96        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
       21.01        25.05         0.99         2.01         2.01         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 
        3.98        12.00        25.97        40.01        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 
       30.02        10.06        54.08         4.01        49.05        12.07 
TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.33         9.67        41.39        40.24 

  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
             0.39              0.39 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
           173.82            154.32 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
           11.770            23.555 
[1] "0.4 - 173.8 (11.8)" "0.4 - 154.3 (23.6)"
[1] "hr=" "1.9"
D9V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CYP11B1 MUTATED          1        6         1         1          3          3
  CYP11B1 WILD-TYPE       28       64        12        25         21          8
                   vv
clus                STAGE IV
  CYP11B1 MUTATED          0
  CYP11B1 WILD-TYPE        3
D9V3, multiclass
            clus
vv           CYP11B1 MUTATED CYP11B1 WILD-TYPE
  STAGE IA                 1                28
  STAGE IB                 6                64
  STAGE IIA                1                12
  STAGE IIB                1                25
  STAGE IIIA               3                21
  STAGE IIIB               3                 8
  STAGE IV                 0                 3
[1] 7 2
[1] 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
  CYP11B1 MUTATED     3  10   1   1
  CYP11B1 WILD-TYPE  34 105  13  11
D9V4, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  T1               3                34
  T2              10               105
  T3               1                13
  T4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CYP11B1 MUTATED     7   3   3   2
  CYP11B1 WILD-TYPE 109  36  14   3
D9V5, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  N0               7               109
  N1               3                36
  N2               3                14
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED    11   0
  CYP11B1 WILD-TYPE 154   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED     11    0
  CYP11B1 WILD-TYPE  154    3
   clus
vv  CYP11B1 MUTATED CYP11B1 WILD-TYPE
  0              11               154
  1               0                 3
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     2  13
  CYP11B1 WILD-TYPE  45 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      2   13
  CYP11B1 WILD-TYPE   45  118
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  FEMALE               2                45
  MALE                13               118
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     7   3
  CYP11B1 WILD-TYPE 113  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      7    3
  CYP11B1 WILD-TYPE  113   17
     clus
vv    CYP11B1 MUTATED CYP11B1 WILD-TYPE
  NO                7               113
  YES               3                17
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CYP11B1 MUTATED                                       1
  CYP11B1 WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CYP11B1 MUTATED                                        0
  CYP11B1 WILD-TYPE                                      1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CYP11B1 MUTATED                                                            14
  CYP11B1 WILD-TYPE                                                         158
D9V10, multiclass
                                                             clus
vv                                                            CYP11B1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              14
                                                             clus
vv                                                            CYP11B1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
                   vv
clus                 R0  R1  R2  RX
  CYP11B1 MUTATED    13   0   1   1
  CYP11B1 WILD-TYPE 134   2   3   9
D9V13, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  R0              13               134
  R1               0                 2
  R2               1                 3
  RX               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP11B1 MUTATED       0                         3     8
  CYP11B1 WILD-TYPE     5                         6   105
D9V14, multiclass
                           clus
vv                          CYP11B1 MUTATED CYP11B1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                   8               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                   cls
clus                 0  1
  CYP11B1 MUTATED    0  8
  CYP11B1 WILD-TYPE  3 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      0    8
  CYP11B1 WILD-TYPE    3   93
                        clus
vv                       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8                93
[1] 2 2
[1] FALSE

Clustering(10) Variable = NOTCH1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  NOTCH1 MUTATED    4 10
  NOTCH1 WILD-TYPE 86 75
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              161 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              10               75 
$`NOTCH1 MUTATED`
TCGA-18-5592 TCGA-21-5782 TCGA-22-1016 TCGA-22-5480 TCGA-22-5485 TCGA-22-5491 
       49.94        31.63        27.02        71.34        30.12        56.32 
TCGA-22-5492 TCGA-33-4583 TCGA-39-5037 TCGA-51-4079 TCGA-66-2759 TCGA-66-2789 
       16.64       151.27        55.56         0.39        25.05         4.04 
TCGA-66-2793 TCGA-66-2795 
       10.06         4.01 

$`NOTCH1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
       36.07        92.42        86.96         2.79       154.32       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
       46.88        60.89        34.78        15.58         9.34        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       33.93        10.82         7.33         4.31         1.74        14.10 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        24.13        38.17        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       19.30        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5482 TCGA-22-5489 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       11.74        62.86        97.94        79.53       173.82       103.53 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       14.07         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
       39.32         4.96         4.01         0.43         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        0.39         3.39       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
       68.38        71.18        39.12        33.11        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       21.47         5.46        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
        4.44        10.65        13.91         0.39        29.95        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       12.43        18.25        21.90        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       35.90        23.57        26.83        11.77        52.67        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       43.10        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       43.99        21.01         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 
       40.01        22.98         5.03        30.02        54.08        49.05 
TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.07        12.33         9.67        41.39        40.24 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.39             0.39 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          151.27           173.82 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           28.57            22.98 
[1] "0.4 - 151.3 (28.6)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.4"
D10V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  NOTCH1 MUTATED          4        3         1         1          2          3
  NOTCH1 WILD-TYPE       25       67        12        25         22          8
                  vv
clus               STAGE IV
  NOTCH1 MUTATED          0
  NOTCH1 WILD-TYPE        3
D10V3, multiclass
            clus
vv           NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE IA                4               25
  STAGE IB                3               67
  STAGE IIA               1               12
  STAGE IIB               1               25
  STAGE IIIA              2               22
  STAGE IIIB              3                8
  STAGE IV                0                3
[1] 7 2
[1] 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
  NOTCH1 MUTATED     6   5   1   2
  NOTCH1 WILD-TYPE  31 110  13  10
D10V4, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T1              6               31
  T2              5              110
  T3              1               13
  T4              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NOTCH1 MUTATED     8   3   2   1
  NOTCH1 WILD-TYPE 108  36  15   4
D10V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0              8              108
  N1              3               36
  N2              2               15
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    13   0
  NOTCH1 WILD-TYPE 152   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     13    0
  NOTCH1 WILD-TYPE  152    3
   clus
vv  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  0             13              152
  1              0                3
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     5   9
  NOTCH1 WILD-TYPE  42 122
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      5    9
  NOTCH1 WILD-TYPE   42  122
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE              5               42
  MALE                9              122
[1] 2 2
[1] FALSE
D10V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     7   2
  NOTCH1 WILD-TYPE 113  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      7    2
  NOTCH1 WILD-TYPE  113   18
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO               7              113
  YES              2               18
[1] 2 2
[1] FALSE
D10V9, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  NOTCH1 MUTATED                                       0
  NOTCH1 WILD-TYPE                                     5
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  NOTCH1 MUTATED                                        0
  NOTCH1 WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NOTCH1 MUTATED                                                            14
  NOTCH1 WILD-TYPE                                                         158
D10V10, multiclass
                                                             clus
vv                                                            NOTCH1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             14
                                                             clus
vv                                                            NOTCH1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, continuous
                  vv
clus                R0  R1  R2  RX
  NOTCH1 MUTATED    14   0   0   0
  NOTCH1 WILD-TYPE 133   2   4  10
D10V13, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  R0             14              133
  R1              0                2
  R2              0                4
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED       0                         1     7
  NOTCH1 WILD-TYPE     5                         8   106
D10V14, multiclass
                           clus
vv                          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              1                8
  WHITE                                  7              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                  cls
clus                0  1
  NOTCH1 MUTATED    0  6
  NOTCH1 WILD-TYPE  3 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      0    6
  NOTCH1 WILD-TYPE    3   95
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6               95
[1] 2 2
[1] FALSE

Clustering(11) Variable = ASB5 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  ASB5 MUTATED    6  3
  ASB5 WILD-TYPE 84 82
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            166 
  ASB5 MUTATED ASB5 WILD-TYPE 
             3             82 
$`ASB5 MUTATED`
TCGA-18-3409 TCGA-33-4533 TCGA-18-3412 TCGA-22-4613 TCGA-33-4538 TCGA-39-5016 
      123.19       133.74        11.34        11.77        97.94       126.58 
TCGA-66-2755 TCGA-66-2766 TCGA-66-2768 
        0.92         1.02         2.01 

$`ASB5 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 
       60.66        64.93       129.01        19.76        17.88        22.49 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        2.79       154.32        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       34.78        15.58         9.34        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        24.13        38.17        34.75        13.12 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
       19.30        63.55        14.63        44.25         0.79        71.34 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
       11.74        30.12        62.86        56.32        16.64        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 
      173.82       103.53       151.27        14.07         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 
       50.66        16.93        44.75        39.32         4.96         4.01 
TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 
        0.43         7.82         6.81         0.39         3.39       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 
        1.94        60.53        68.38        71.18        55.56        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 
       33.11        22.98        24.89        21.47         5.46        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        0.39         0.39        29.95        28.96        12.43        18.25 
TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       21.90        10.22        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       56.91        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       26.83        11.77        52.67        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        0.99         2.01         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         2.01        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
        1.97        25.97        40.01        22.98         4.04         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 
       30.02        10.06        54.08         4.01        49.05        12.07 
TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.33         9.67        41.39        40.24 

  ASB5 MUTATED ASB5 WILD-TYPE 
          0.92           0.39 
  ASB5 MUTATED ASB5 WILD-TYPE 
        133.74         173.82 
  ASB5 MUTATED ASB5 WILD-TYPE 
        11.770         23.555 
[1] "0.9 - 133.7 (11.8)" "0.4 - 173.8 (23.6)"
[1] "hr=" "2"  
D11V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ASB5 MUTATED          2        3         1         1          2          0
  ASB5 WILD-TYPE       27       67        12        25         22         11
                vv
clus             STAGE IV
  ASB5 MUTATED          0
  ASB5 WILD-TYPE        3
D11V3, multiclass
            clus
vv           ASB5 MUTATED ASB5 WILD-TYPE
  STAGE IA              2             27
  STAGE IB              3             67
  STAGE IIA             1             12
  STAGE IIB             1             25
  STAGE IIIA            2             22
  STAGE IIIB            0             11
  STAGE IV              0              3
[1] 7 2
[1] 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
  ASB5 MUTATED     2   7   0   0
  ASB5 WILD-TYPE  35 108  14  12
D11V4, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  T1            2             35
  T2            7            108
  T3            0             14
  T4            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ASB5 MUTATED     5   2   2   0
  ASB5 WILD-TYPE 111  37  15   5
D11V5, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  N0            5            111
  N1            2             37
  N2            2             15
  N3            0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                cls
clus               0   1
  ASB5 MUTATED     9   0
  ASB5 WILD-TYPE 156   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      9    0
  ASB5 WILD-TYPE  156    3
   clus
vv  ASB5 MUTATED ASB5 WILD-TYPE
  0            9            156
  1            0              3
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  ASB5 MUTATED     2   7
  ASB5 WILD-TYPE  45 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      2    7
  ASB5 WILD-TYPE   45  124
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  FEMALE            2             45
  MALE              7            124
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  ASB5 MUTATED     6   0
  ASB5 WILD-TYPE 114  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      6    0
  ASB5 WILD-TYPE  114   20
     clus
vv    ASB5 MUTATED ASB5 WILD-TYPE
  NO             6            114
  YES            0             20
[1] 2 2
[1] FALSE
D11V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  ASB5 MUTATED                                       2
  ASB5 WILD-TYPE                                     3
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  ASB5 MUTATED                                        0
  ASB5 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASB5 MUTATED                                                             7
  ASB5 WILD-TYPE                                                         165
D11V10, multiclass
                                                             clus
vv                                                            ASB5 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
                                                             clus
vv                                                            ASB5 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
                vv
clus              R0  R1  R2  RX
  ASB5 MUTATED     8   0   0   1
  ASB5 WILD-TYPE 139   2   4   9
D11V13, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  R0            8            139
  R1            0              2
  R2            0              4
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASB5 MUTATED       0                         1     5
  ASB5 WILD-TYPE     5                         8   108
D11V14, multiclass
                           clus
vv                          ASB5 MUTATED ASB5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                                5            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                cls
clus              0  1
  ASB5 MUTATED    1  3
  ASB5 WILD-TYPE  2 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      1    3
  ASB5 WILD-TYPE    2   98
                        clus
vv                       ASB5 MUTATED ASB5 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            3             98
[1] 2 2
[1] FALSE

Clustering(12) Variable = IRF6 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2             0  1
  IRF6 MUTATED    2  4
  IRF6 WILD-TYPE 88 81
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            169 
  IRF6 MUTATED IRF6 WILD-TYPE 
             4             81 
$`IRF6 MUTATED`
TCGA-22-1002 TCGA-33-4566 TCGA-34-5231 TCGA-39-5028 TCGA-60-2710 TCGA-66-2778 
        4.31       173.82        65.23         1.71        66.54        19.00 

$`IRF6 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
      119.54        46.88        60.89        34.78        15.58         9.34 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1011 
       31.63        41.69        33.93        10.82         7.33         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
       14.10        27.02        20.48        35.08        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       34.75        13.12        19.30        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25         0.79        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
       56.32        16.64        97.94        79.53       103.53       151.27 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
       14.07         2.63        61.61        32.88        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        4.96         4.01         0.43         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        3.39       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
      102.18        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        5.46        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
       10.65        13.91         0.39         0.39        29.95        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       12.43        18.25        21.90        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       49.48        56.91        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
       23.57        26.83        11.77        52.67        16.96        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        2.01        23.01        19.00         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
        4.01        49.05        12.07        12.33         9.67        41.39 
TCGA-85-6561 
       40.24 

  IRF6 MUTATED IRF6 WILD-TYPE 
          1.71           0.39 
  IRF6 MUTATED IRF6 WILD-TYPE 
        173.82         154.32 
  IRF6 MUTATED IRF6 WILD-TYPE 
        42.115         23.540 
[1] "1.7 - 173.8 (42.1)" "0.4 - 154.3 (23.5)"
[1] "hr=" "1.4"
D12V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  IRF6 MUTATED          2        1         1         0          1          1
  IRF6 WILD-TYPE       27       69        12        26         23         10
                vv
clus             STAGE IV
  IRF6 MUTATED          0
  IRF6 WILD-TYPE        3
D12V3, multiclass
            clus
vv           IRF6 MUTATED IRF6 WILD-TYPE
  STAGE IA              2             27
  STAGE IB              1             69
  STAGE IIA             1             12
  STAGE IIB             0             26
  STAGE IIIA            1             23
  STAGE IIIB            1             10
  STAGE IV              0              3
[1] 7 2
[1] 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
  IRF6 MUTATED     3   2   0   1
  IRF6 WILD-TYPE  34 113  14  11
D12V4, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  T1            3             34
  T2            2            113
  T3            0             14
  T4            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRF6 MUTATED     3   2   0   1
  IRF6 WILD-TYPE 113  37  17   4
D12V5, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  N0            3            113
  N1            2             37
  N2            0             17
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                cls
clus               0   1
  IRF6 MUTATED     6   0
  IRF6 WILD-TYPE 159   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      6    0
  IRF6 WILD-TYPE  159    3
   clus
vv  IRF6 MUTATED IRF6 WILD-TYPE
  0            6            159
  1            0              3
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  IRF6 MUTATED     2   4
  IRF6 WILD-TYPE  45 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      2    4
  IRF6 WILD-TYPE   45  127
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  FEMALE            2             45
  MALE              4            127
[1] 2 2
[1] FALSE
D12V8, binary
                cls
clus               0   1
  IRF6 MUTATED     4   1
  IRF6 WILD-TYPE 116  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      4    1
  IRF6 WILD-TYPE  116   19
     clus
vv    IRF6 MUTATED IRF6 WILD-TYPE
  NO             4            116
  YES            1             19
[1] 2 2
[1] FALSE
D12V9, continuous
[1] "Remove cluster labels:" "IRF6 MUTATED"          
clus
  IRF6 MUTATED IRF6 WILD-TYPE 
             1             58 
    TCGA-18-3406     TCGA-18-3407     TCGA-18-3410     TCGA-18-4083 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5472     TCGA-33-4533     TCGA-60-2711     TCGA-60-2712 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-60-2715     TCGA-60-2721     TCGA-18-3408     TCGA-18-3412 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-18-3414     TCGA-21-1081     TCGA-21-5782     TCGA-21-5787 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-4591     TCGA-22-4593     TCGA-22-4595     TCGA-22-4599 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-4601     TCGA-22-4604     TCGA-22-4613     TCGA-22-5473 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5474     TCGA-22-5477     TCGA-22-5478     TCGA-22-5480 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5482     TCGA-22-5485     TCGA-22-5489     TCGA-22-5491 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5492     TCGA-33-4538     TCGA-33-4547     TCGA-33-4582 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-33-4583     TCGA-33-4586     TCGA-34-5234     TCGA-37-4133 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-37-4135     TCGA-37-5819     TCGA-43-3394     TCGA-43-6143 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-43-6647     TCGA-43-6770     TCGA-46-3768     TCGA-60-2698 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-60-2713     TCGA-60-2719     TCGA-60-2723     TCGA-60-2725 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5131     TCGA-70-6722     TCGA-70-6723 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  IRF6 MUTATED                                       0
  IRF6 WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  IRF6 MUTATED                                        0
  IRF6 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IRF6 MUTATED                                                             6
  IRF6 WILD-TYPE                                                         166
D12V10, multiclass
                                                             clus
vv                                                            IRF6 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
                                                             clus
vv                                                            IRF6 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
                vv
clus              R0  R1  R2  RX
  IRF6 MUTATED     3   0   1   0
  IRF6 WILD-TYPE 144   2   3  10
D12V13, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  R0            3            144
  R1            0              2
  R2            1              3
  RX            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRF6 MUTATED       0                         0     5
  IRF6 WILD-TYPE     5                         9   108
D12V14, multiclass
                           clus
vv                          IRF6 MUTATED IRF6 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                5            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                cls
clus              0  1
  IRF6 MUTATED    0  5
  IRF6 WILD-TYPE  3 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      0    5
  IRF6 WILD-TYPE    3   96
                        clus
vv                       IRF6 MUTATED IRF6 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5             96
[1] 2 2
[1] FALSE

Clustering(13) Variable = EP300 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  EP300 MUTATED    5  3
  EP300 WILD-TYPE 85 82
  EP300 MUTATED EP300 WILD-TYPE 
              8             167 
  EP300 MUTATED EP300 WILD-TYPE 
              3              82 
$`EP300 MUTATED`
TCGA-18-3419 TCGA-21-5786 TCGA-22-4595 TCGA-37-3783 TCGA-56-1622 TCGA-60-2713 
       92.42        33.93        24.13         4.01        28.96        56.91 
TCGA-66-2763 TCGA-66-2773 
        0.99         3.02 

$`EP300 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       36.07        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
       46.88        60.89        34.78        15.58         9.34        31.63 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       41.69        10.82         7.33         4.31         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       27.02        20.48        35.08        38.17        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       19.30        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.96         0.43         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        5.46        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-5897 
       10.65        13.91         0.39         0.39        29.95        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       18.25        21.90        10.22        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       66.54        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       26.83        11.77        52.67        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        0.99         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
       25.05         2.01         1.02         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.07        12.33         9.67        41.39        40.24 

  EP300 MUTATED EP300 WILD-TYPE 
           0.99            0.39 
  EP300 MUTATED EP300 WILD-TYPE 
          92.42          173.82 
  EP300 MUTATED EP300 WILD-TYPE 
         26.545          23.010 
[1] "1.0 - 92.4 (26.5)"  "0.4 - 173.8 (23.0)"
[1] "hr=" "1.1"
D13V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  EP300 MUTATED          0        5         0         1          2          0
  EP300 WILD-TYPE       29       65        13        25         22         11
                 vv
clus              STAGE IV
  EP300 MUTATED          0
  EP300 WILD-TYPE        3
D13V3, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE IA               0              29
  STAGE IB               5              65
  STAGE IIA              0              13
  STAGE IIB              1              25
  STAGE IIIA             2              22
  STAGE IIIB             0              11
  STAGE IV               0               3
[1] 7 2
[1] 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
  EP300 MUTATED     0   6   2   0
  EP300 WILD-TYPE  37 109  12  12
D13V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             0              37
  T2             6             109
  T3             2              12
  T4             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EP300 MUTATED     5   1   2   0
  EP300 WILD-TYPE 111  38  15   5
D13V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0             5             111
  N1             1              38
  N2             2              15
  N3             0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  EP300 MUTATED     7   0
  EP300 WILD-TYPE 158   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      7    0
  EP300 WILD-TYPE  158    3
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0             7             158
  1             0               3
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  EP300 MUTATED     1   7
  EP300 WILD-TYPE  46 124
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      1    7
  EP300 WILD-TYPE   46  124
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE             1              46
  MALE               7             124
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  EP300 MUTATED     3   1
  EP300 WILD-TYPE 117  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      3    1
  EP300 WILD-TYPE  117   19
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              3             117
  YES             1              19
[1] 2 2
[1] FALSE
D13V9, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              57 
     TCGA-18-3406      TCGA-18-3407      TCGA-18-3410      TCGA-18-4083 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5472      TCGA-33-4533      TCGA-60-2711      TCGA-60-2712 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-60-2715      TCGA-60-2721      TCGA-18-3408      TCGA-18-3412 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-18-3414      TCGA-21-1081      TCGA-21-5782      TCGA-21-5787 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-4591      TCGA-22-4593      TCGA-22-4599      TCGA-22-4601 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-4604      TCGA-22-4613      TCGA-22-5473      TCGA-22-5474 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5477      TCGA-22-5478      TCGA-22-5480      TCGA-22-5482 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5485      TCGA-22-5489      TCGA-22-5491      TCGA-22-5492 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-33-4538      TCGA-33-4547      TCGA-33-4582      TCGA-33-4583 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-33-4586      TCGA-34-5234      TCGA-37-4133      TCGA-37-4135 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-37-5819      TCGA-43-3394      TCGA-43-6143      TCGA-43-6647 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6770      TCGA-46-3768      TCGA-60-2698      TCGA-60-2710 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-60-2719      TCGA-60-2723      TCGA-60-2725      TCGA-60-2726 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-63-5131      TCGA-70-6722      TCGA-70-6723      TCGA-85-6560 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6561 
"EP300 WILD-TYPE" 
                 vv
clus              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  EP300 MUTATED                                       0
  EP300 WILD-TYPE                                     5
                 vv
clus              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  EP300 MUTATED                                        0
  EP300 WILD-TYPE                                      1
                 vv
clus              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EP300 MUTATED                                                             8
  EP300 WILD-TYPE                                                         164
D13V10, multiclass
                                                             clus
vv                                                            EP300 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
                                                             clus
vv                                                            EP300 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED     8   0   0   0
  EP300 WILD-TYPE 139   2   4  10
D13V13, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0             8             139
  R1             0               2
  R2             0               4
  RX             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED       0                         0     5
  EP300 WILD-TYPE     5                         9   108
D13V14, multiclass
                           clus
vv                          EP300 MUTATED EP300 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               9
  WHITE                                 5             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                 cls
clus               0  1
  EP300 MUTATED    0  4
  EP300 WILD-TYPE  3 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      0    4
  EP300 WILD-TYPE    3   97
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4              97
[1] 2 2
[1] FALSE

Clustering(14) Variable = CPS1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  CPS1 MUTATED   13 11
  CPS1 WILD-TYPE 77 74
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            151 
  CPS1 MUTATED CPS1 WILD-TYPE 
            11             74 
$`CPS1 MUTATED`
TCGA-18-3409 TCGA-18-3415 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
      123.19        92.15        92.42        49.94       119.54        46.88 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-5784 TCGA-22-4591 TCGA-22-5482 
       60.89        34.78         9.34        41.69        20.48        11.74 
TCGA-34-5236 TCGA-39-5016 TCGA-46-6026 TCGA-51-4080 TCGA-60-2698 TCGA-60-2720 
        9.07       126.58        13.91         0.39        10.22         3.19 
TCGA-60-2722 TCGA-66-2757 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-85-6560 
       29.85        43.99         1.97        25.97         4.04        41.39 

$`CPS1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 
       60.66        64.93       129.01       133.74        19.76        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       22.49        18.38        41.42         9.01        35.34        32.32 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       75.75       117.57        11.34        23.54        36.07        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1078 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
        2.79       154.32        15.58        31.63        33.93        10.82 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 
        7.33         4.31         1.74        14.10        27.02        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
       24.13        38.17        34.75        13.12        19.30        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 
       63.55        14.63        44.25         0.79        71.34        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      103.53       151.27        14.07         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        81.24        74.66        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
       44.75        39.32         4.96         4.01         0.43         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        6.81         0.39         3.39       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 
       68.38        71.18        55.56        39.12        33.11        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       24.89        21.47         5.46        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-56-1622 
        9.83         4.44        10.65         0.39        29.95        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       12.43        18.25        21.90        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       66.54        56.91        42.64        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
       11.77        52.67        16.96        43.10        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92         0.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        3.02         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       24.95        40.01        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 
       54.08         4.01        49.05        12.07        12.33         9.67 
TCGA-85-6561 
       40.24 

  CPS1 MUTATED CPS1 WILD-TYPE 
          0.39           0.39 
  CPS1 MUTATED CPS1 WILD-TYPE 
        126.58         173.82 
  CPS1 MUTATED CPS1 WILD-TYPE 
        32.315         22.980 
[1] "0.4 - 126.6 (32.3)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.2"
D14V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CPS1 MUTATED          3        7         2         8          2          2
  CPS1 WILD-TYPE       26       63        11        18         22          9
                vv
clus             STAGE IV
  CPS1 MUTATED          0
  CPS1 WILD-TYPE        3
D14V3, multiclass
            clus
vv           CPS1 MUTATED CPS1 WILD-TYPE
  STAGE IA              3             26
  STAGE IB              7             63
  STAGE IIA             2             11
  STAGE IIB             8             18
  STAGE IIIA            2             22
  STAGE IIIB            2              9
  STAGE IV              0              3
[1] 7 2
[1] 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
  CPS1 MUTATED     5  14   4   1
  CPS1 WILD-TYPE  32 101  10  11
D14V4, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  T1            5             32
  T2           14            101
  T3            4             10
  T4            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CPS1 MUTATED    13   9   1   1
  CPS1 WILD-TYPE 103  30  16   4
D14V5, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  N0           13            103
  N1            9             30
  N2            1             16
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                cls
clus               0   1
  CPS1 MUTATED    23   0
  CPS1 WILD-TYPE 142   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     23    0
  CPS1 WILD-TYPE  142    3
   clus
vv  CPS1 MUTATED CPS1 WILD-TYPE
  0           23            142
  1            0              3
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  CPS1 MUTATED     6  18
  CPS1 WILD-TYPE  41 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      6   18
  CPS1 WILD-TYPE   41  113
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  FEMALE            6             41
  MALE             18            113
[1] 2 2
[1] FALSE
D14V8, binary
                cls
clus               0   1
  CPS1 MUTATED    16   4
  CPS1 WILD-TYPE 104  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     16    4
  CPS1 WILD-TYPE  104   16
     clus
vv    CPS1 MUTATED CPS1 WILD-TYPE
  NO            16            104
  YES            4             16
[1] 2 2
[1] FALSE
D14V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CPS1 MUTATED                                       3
  CPS1 WILD-TYPE                                     2
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CPS1 MUTATED                                        0
  CPS1 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CPS1 MUTATED                                                            21
  CPS1 WILD-TYPE                                                         151
D14V10, multiclass
                                                             clus
vv                                                            CPS1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           21
                                                             clus
vv                                                            CPS1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
                vv
clus              R0  R1  R2  RX
  CPS1 MUTATED    21   0   1   1
  CPS1 WILD-TYPE 126   2   3   9
D14V13, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  R0           21            126
  R1            0              2
  R2            1              3
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPS1 MUTATED       0                         2    15
  CPS1 WILD-TYPE     5                         7    98
D14V14, multiclass
                           clus
vv                          CPS1 MUTATED CPS1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            2              7
  WHITE                               15             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                cls
clus              0  1
  CPS1 MUTATED    0 13
  CPS1 WILD-TYPE  3 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      0   13
  CPS1 WILD-TYPE    3   88
                        clus
vv                       CPS1 MUTATED CPS1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13             88
[1] 2 2
[1] FALSE

Clustering(15) Variable = ARID1A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    6  6
  ARID1A WILD-TYPE 84 79
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              163 
  ARID1A MUTATED ARID1A WILD-TYPE 
               6               79 
$`ARID1A MUTATED`
TCGA-18-3409 TCGA-39-5039 TCGA-21-1078 TCGA-39-5022 TCGA-39-5037 TCGA-43-3394 
      123.19        17.88        15.58        55.20        55.56        39.12 
TCGA-51-4080 TCGA-51-4081 TCGA-60-2720 TCGA-63-6202 TCGA-66-2756 TCGA-66-2793 
        0.39        29.95         3.19        52.67         0.99        10.06 

$`ARID1A WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-43-2578 
       60.66        64.93       129.01       133.74        19.76        22.49 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       60.89        34.78         9.34        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        24.13        38.17        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       19.30        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        4.96         4.01         0.43         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 
        3.39       126.58       111.35        68.58        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 
       33.11        22.98        24.89        21.47         5.46        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 
        0.39        28.96        12.43        18.25        21.90        10.22 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 
       21.93        80.45        49.48        66.54        56.91        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-66-2727 
       29.85        35.90        23.57        26.83        11.77        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       43.10        21.07         0.99         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
       40.01        22.98         4.04         5.03        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
        4.01        49.05        12.07        12.33         9.67        41.39 
TCGA-85-6561 
       40.24 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.39             0.39 
  ARID1A MUTATED ARID1A WILD-TYPE 
          123.19           173.82 
  ARID1A MUTATED ARID1A WILD-TYPE 
          23.915           23.540 
[1] "0.4 - 123.2 (23.9)" "0.4 - 173.8 (23.5)"
[1] "hr=" "1.1"
D15V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ARID1A MUTATED          1        5         3         1          0          3
  ARID1A WILD-TYPE       28       65        10        25         24          8
                  vv
clus               STAGE IV
  ARID1A MUTATED          0
  ARID1A WILD-TYPE        3
D15V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE IA                1               28
  STAGE IB                5               65
  STAGE IIA               3               10
  STAGE IIB               1               25
  STAGE IIIA              0               24
  STAGE IIIB              3                8
  STAGE IV                0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     2   8   0   3
  ARID1A WILD-TYPE  35 107  14   9
D15V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2               35
  T2              8              107
  T3              0               14
  T4              3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1A MUTATED     9   4   0   0
  ARID1A WILD-TYPE 107  35  17   5
D15V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              9              107
  N1              4               35
  N2              0               17
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    12   0
  ARID1A WILD-TYPE 153   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     12    0
  ARID1A WILD-TYPE  153    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             12              153
  1              0                3
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  12
  ARID1A WILD-TYPE  46 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   12
  ARID1A WILD-TYPE   46  119
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              1               46
  MALE               12              119
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    10   0
  ARID1A WILD-TYPE 110  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     10    0
  ARID1A WILD-TYPE  110   20
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              10              110
  YES              0               20
[1] 2 2
[1] FALSE
D15V9, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               58 
      TCGA-18-3406       TCGA-18-3407       TCGA-18-3410       TCGA-18-4083 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5472       TCGA-33-4533       TCGA-60-2711       TCGA-60-2712 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2715       TCGA-60-2721       TCGA-18-3408       TCGA-18-3412 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-18-3414       TCGA-21-1081       TCGA-21-5782       TCGA-21-5787 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-4591       TCGA-22-4593       TCGA-22-4595       TCGA-22-4599 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-4601       TCGA-22-4604       TCGA-22-4613       TCGA-22-5473 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5474       TCGA-22-5477       TCGA-22-5478       TCGA-22-5480 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5482       TCGA-22-5485       TCGA-22-5489       TCGA-22-5491 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5492       TCGA-33-4538       TCGA-33-4547       TCGA-33-4582 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-33-4583       TCGA-33-4586       TCGA-34-5234       TCGA-37-4133 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-37-4135       TCGA-37-5819       TCGA-43-6143       TCGA-43-6647 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-43-6770       TCGA-46-3768       TCGA-60-2698       TCGA-60-2710 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2713       TCGA-60-2719       TCGA-60-2723       TCGA-60-2725 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2726       TCGA-63-5131       TCGA-70-6722       TCGA-70-6723 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-85-6560       TCGA-85-6561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  ARID1A MUTATED                                       2
  ARID1A WILD-TYPE                                     3
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  ARID1A MUTATED                                        0
  ARID1A WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                            11
  ARID1A WILD-TYPE                                                         161
D15V10, multiclass
                                                             clus
vv                                                            ARID1A MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
                                                             clus
vv                                                            ARID1A WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
D15V12, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    13   0   0   0
  ARID1A WILD-TYPE 134   2   4  10
D15V13, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             13              134
  R1              0                2
  R2              0                4
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         2     7
  ARID1A WILD-TYPE     5                         7   106
D15V14, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                  7              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  8
  ARID1A WILD-TYPE  3 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    8
  ARID1A WILD-TYPE    3   93
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8               93
[1] 2 2
[1] FALSE

Clustering(16) Variable = SLC28A1 MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  SLC28A1 MUTATED    6  3
  SLC28A1 WILD-TYPE 84 82
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               166 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                3                82 
$`SLC28A1 MUTATED`
TCGA-18-3409 TCGA-22-5472 TCGA-18-3412 TCGA-34-5232 TCGA-34-5239 TCGA-34-5928 
      123.19        64.93        11.34        81.24        60.30        39.32 
TCGA-39-5028 TCGA-46-3767 TCGA-66-2785 
        1.71        13.02         1.97 

$`SLC28A1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-5471 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 
       60.66       129.01       133.74        19.76        17.88        22.49 
TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-18-3408 
       18.38        41.42         9.01        35.34        32.32        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        2.79       154.32        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       34.78        15.58         9.34        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        24.13        38.17        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       19.30        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 
        2.63        61.61        32.88        65.23        74.66         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 
       50.66        16.93        44.75         4.96         4.01         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         0.39         3.39       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
       68.58        55.20        82.52       102.18        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 
       60.53        68.38        71.18        55.56        39.12        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 
       22.98        24.89        21.47         5.46        13.32        12.16 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.83         4.44        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 
       29.95        28.96        12.43        18.25        21.90        10.22 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 
       21.93        80.45        49.48        66.54        56.91        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        3.19        29.85        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       52.67        16.96        43.10        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        3.02         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
       24.95        25.97        40.01        22.98         4.04         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 
       30.02        10.06        54.08         4.01        49.05        12.07 
TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       12.33         9.67        41.39        40.24 

  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
             1.71              0.39 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
           123.19            173.82 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
           39.320            23.275 
[1] "1.7 - 123.2 (39.3)" "0.4 - 173.8 (23.3)"
[1] "hr=" "1.7"
D16V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  SLC28A1 MUTATED          2        3         1         1          2          0
  SLC28A1 WILD-TYPE       27       67        12        25         22         11
                   vv
clus                STAGE IV
  SLC28A1 MUTATED          0
  SLC28A1 WILD-TYPE        3
D16V3, multiclass
            clus
vv           SLC28A1 MUTATED SLC28A1 WILD-TYPE
  STAGE IA                 2                27
  STAGE IB                 3                67
  STAGE IIA                1                12
  STAGE IIB                1                25
  STAGE IIIA               2                22
  STAGE IIIB               0                11
  STAGE IV                 0                 3
[1] 7 2
[1] 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
  SLC28A1 MUTATED     3   4   0   2
  SLC28A1 WILD-TYPE  34 111  14  10
D16V4, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  T1               3                34
  T2               4               111
  T3               0                14
  T4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC28A1 MUTATED     6   3   0   0
  SLC28A1 WILD-TYPE 110  36  17   5
D16V5, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  N0               6               110
  N1               3                36
  N2               0                17
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  SLC28A1 MUTATED     9   0
  SLC28A1 WILD-TYPE 156   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      9    0
  SLC28A1 WILD-TYPE  156    3
   clus
vv  SLC28A1 MUTATED SLC28A1 WILD-TYPE
  0               9               156
  1               0                 3
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  SLC28A1 MUTATED     2   7
  SLC28A1 WILD-TYPE  45 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      2    7
  SLC28A1 WILD-TYPE   45  124
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  FEMALE               2                45
  MALE                 7               124
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  SLC28A1 MUTATED     7   0
  SLC28A1 WILD-TYPE 113  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      7    0
  SLC28A1 WILD-TYPE  113   20
     clus
vv    SLC28A1 MUTATED SLC28A1 WILD-TYPE
  NO                7               113
  YES               0                20
[1] 2 2
[1] FALSE
D16V9, continuous
[1] "Remove cluster labels:" "SLC28A1 MUTATED"       
clus
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                2                57 
       TCGA-18-3406        TCGA-18-3407        TCGA-18-3410        TCGA-18-4083 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-33-4533        TCGA-60-2711        TCGA-60-2712        TCGA-60-2715 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2721        TCGA-18-3408        TCGA-18-3414        TCGA-21-1081 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-21-5782        TCGA-21-5787        TCGA-22-4591        TCGA-22-4593 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-4595        TCGA-22-4599        TCGA-22-4601        TCGA-22-4604 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-4613        TCGA-22-5473        TCGA-22-5474        TCGA-22-5477 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-5478        TCGA-22-5480        TCGA-22-5482        TCGA-22-5485 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-5489        TCGA-22-5491        TCGA-22-5492        TCGA-33-4538 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-33-4547        TCGA-33-4582        TCGA-33-4583        TCGA-33-4586 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-34-5234        TCGA-37-4133        TCGA-37-4135        TCGA-37-5819 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-43-3394        TCGA-43-6143        TCGA-43-6647        TCGA-43-6770 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-46-3768        TCGA-60-2698        TCGA-60-2710        TCGA-60-2713 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2719        TCGA-60-2723        TCGA-60-2725        TCGA-60-2726 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-63-5131        TCGA-70-6722        TCGA-70-6723        TCGA-85-6560 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-85-6561 
"SLC28A1 WILD-TYPE" 
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  SLC28A1 MUTATED                                       1
  SLC28A1 WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  SLC28A1 MUTATED                                        0
  SLC28A1 WILD-TYPE                                      1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC28A1 MUTATED                                                             8
  SLC28A1 WILD-TYPE                                                         164
D16V10, multiclass
                                                             clus
vv                                                            SLC28A1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               8
                                                             clus
vv                                                            SLC28A1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
[1] "Remove cluster labels:" "SLC28A1 MUTATED"       
clus
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                2               104 
       TCGA-18-3406        TCGA-33-4533        TCGA-39-5039        TCGA-43-2578 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2711        TCGA-60-2712        TCGA-60-2715        TCGA-60-2721 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-18-3417        TCGA-21-1078        TCGA-21-5782        TCGA-21-5786 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-21-5787        TCGA-22-0944        TCGA-22-1002        TCGA-22-1011 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-1012        TCGA-22-1016        TCGA-22-4591        TCGA-22-4593 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-4607        TCGA-22-4613        TCGA-22-5473        TCGA-22-5474 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-5480        TCGA-22-5482        TCGA-22-5492        TCGA-33-4547 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-33-4582        TCGA-33-4583        TCGA-33-4586        TCGA-34-5234 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-34-5240        TCGA-34-5241        TCGA-37-4133        TCGA-37-4135 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-37-5819        TCGA-39-5021        TCGA-39-5022        TCGA-39-5024 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-39-5027        TCGA-39-5029        TCGA-39-5030        TCGA-39-5031 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-39-5035        TCGA-39-5036        TCGA-39-5037        TCGA-43-3394 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-43-3920        TCGA-43-6143        TCGA-43-6647        TCGA-43-6770 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-43-6771        TCGA-56-1622        TCGA-56-5898        TCGA-56-6545 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-56-6546        TCGA-60-2707        TCGA-60-2708        TCGA-60-2709 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2710        TCGA-60-2713        TCGA-60-2719        TCGA-60-2720 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2723        TCGA-60-2724        TCGA-60-2725        TCGA-60-2726 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-63-6202        TCGA-66-2727        TCGA-66-2734        TCGA-66-2742 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2744        TCGA-66-2754        TCGA-66-2755        TCGA-66-2756 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2757        TCGA-66-2758        TCGA-66-2759        TCGA-66-2763 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2765        TCGA-66-2766        TCGA-66-2767        TCGA-66-2770 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2771        TCGA-66-2773        TCGA-66-2777        TCGA-66-2778 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2780        TCGA-66-2781        TCGA-66-2782        TCGA-66-2783 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2786        TCGA-66-2787        TCGA-66-2788        TCGA-66-2789 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2791        TCGA-66-2792        TCGA-66-2793        TCGA-66-2794 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-66-2795        TCGA-66-2800        TCGA-85-6560        TCGA-85-6561 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  SLC28A1 MUTATED     6   0   0   0
  SLC28A1 WILD-TYPE 141   2   4  10
D16V13, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  R0               6               141
  R1               0                 2
  R2               0                 4
  RX               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC28A1 MUTATED       0                         1     7
  SLC28A1 WILD-TYPE     5                         8   106
D16V14, multiclass
                           clus
vv                          SLC28A1 MUTATED SLC28A1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   7               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                   cls
clus                 0  1
  SLC28A1 MUTATED    0  8
  SLC28A1 WILD-TYPE  3 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      0    8
  SLC28A1 WILD-TYPE    3   93
                        clus
vv                       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8                93
[1] 2 2
[1] FALSE

Clustering(17) Variable = POLR2B MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2               0  1
  POLR2B MUTATED    1  5
  POLR2B WILD-TYPE 89 80
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              169 
  POLR2B MUTATED POLR2B WILD-TYPE 
               5               80 
$`POLR2B MUTATED`
TCGA-22-4604 TCGA-22-5478 TCGA-22-5492 TCGA-34-2600 TCGA-66-2773 TCGA-85-6561 
       13.12         0.79        16.64        61.61         3.02        40.24 

$`POLR2B WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
      119.54        46.88        60.89        34.78        15.58         9.34 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       31.63        41.69        33.93        10.82         7.33         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
        1.74        14.10        27.02        20.48        35.08        24.13 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       38.17        34.75        19.30        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       44.25        71.34        11.74        30.12        62.86        56.32 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.01         0.43         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        5.46        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
       10.65        13.91         0.39         0.39        29.95        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       12.43        18.25        21.90        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       35.90        23.57        26.83        11.77        52.67        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       43.10        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
       43.99        21.01        25.05         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        2.01         2.01        23.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       40.01        22.98         4.04         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 
       54.08         4.01        49.05        12.07        12.33         9.67 
TCGA-85-6560 
       41.39 

  POLR2B MUTATED POLR2B WILD-TYPE 
            0.79             0.39 
  POLR2B MUTATED POLR2B WILD-TYPE 
           61.61           173.82 
  POLR2B MUTATED POLR2B WILD-TYPE 
           14.88            23.57 
[1] "0.8 - 61.6 (14.9)"  "0.4 - 173.8 (23.6)"
[1] "hr=" "2.6"
D17V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  POLR2B MUTATED          1        3         1         0          1          0
  POLR2B WILD-TYPE       28       67        12        26         23         11
                  vv
clus               STAGE IV
  POLR2B MUTATED          0
  POLR2B WILD-TYPE        3
D17V3, multiclass
            clus
vv           POLR2B MUTATED POLR2B WILD-TYPE
  STAGE IA                1               28
  STAGE IB                3               67
  STAGE IIA               1               12
  STAGE IIB               0               26
  STAGE IIIA              1               23
  STAGE IIIB              0               11
  STAGE IV                0                3
[1] 7 2
[1] 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
  POLR2B MUTATED     1   5   0   0
  POLR2B WILD-TYPE  36 110  14  12
D17V4, multiclass
    clus
vv   POLR2B MUTATED POLR2B WILD-TYPE
  T1              1               36
  T2              5              110
  T3              0               14
  T4              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  POLR2B MUTATED     3   1   1   0
  POLR2B WILD-TYPE 113  38  16   5
D17V5, multiclass
    clus
vv   POLR2B MUTATED POLR2B WILD-TYPE
  N0              3              113
  N1              1               38
  N2              1               16
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                  cls
clus                 0   1
  POLR2B MUTATED     6   0
  POLR2B WILD-TYPE 159   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      6    0
  POLR2B WILD-TYPE  159    3
   clus
vv  POLR2B MUTATED POLR2B WILD-TYPE
  0              6              159
  1              0                3
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  POLR2B MUTATED     2   4
  POLR2B WILD-TYPE  45 127
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      2    4
  POLR2B WILD-TYPE   45  127
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  FEMALE              2               45
  MALE                4              127
[1] 2 2
[1] FALSE
D17V8, binary
                  cls
clus                 0   1
  POLR2B MUTATED     3   1
  POLR2B WILD-TYPE 117  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      3    1
  POLR2B WILD-TYPE  117   19
     clus
vv    POLR2B MUTATED POLR2B WILD-TYPE
  NO               3              117
  YES              1               19
[1] 2 2
[1] FALSE
D17V9, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  POLR2B MUTATED                                       0
  POLR2B WILD-TYPE                                     5
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  POLR2B MUTATED                                        0
  POLR2B WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  POLR2B MUTATED                                                             6
  POLR2B WILD-TYPE                                                         166
D17V10, multiclass
                                                             clus
vv                                                            POLR2B MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
                                                             clus
vv                                                            POLR2B WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
                  vv
clus                R0  R1  R2  RX
  POLR2B MUTATED     6   0   0   0
  POLR2B WILD-TYPE 141   2   4  10
D17V13, multiclass
    clus
vv   POLR2B MUTATED POLR2B WILD-TYPE
  R0              6              141
  R1              0                2
  R2              0                4
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POLR2B MUTATED       0                         0     3
  POLR2B WILD-TYPE     5                         9   110
D17V14, multiclass
                           clus
vv                          POLR2B MUTATED POLR2B WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  3              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                  cls
clus                0  1
  POLR2B MUTATED    0  2
  POLR2B WILD-TYPE  3 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      0    2
  POLR2B WILD-TYPE    3   99
                        clus
vv                       POLR2B MUTATED POLR2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              2               99
[1] 2 2
[1] FALSE

Clustering(18) Variable = HRAS MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  HRAS MUTATED    3  2
  HRAS WILD-TYPE 87 83
  HRAS MUTATED HRAS WILD-TYPE 
             5            170 
  HRAS MUTATED HRAS WILD-TYPE 
             2             83 
$`HRAS MUTATED`
TCGA-18-3414 TCGA-21-5786 TCGA-34-2600 TCGA-34-5240 TCGA-66-2758 
       23.54        33.93        61.61        50.66        21.01 

$`HRAS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 
       32.32        75.75       117.57        11.34        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
       46.88        60.89        34.78        15.58         9.34        31.63 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       41.69        10.82         7.33         4.31         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       27.02        20.48        35.08        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       13.12        19.30        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        0.79        71.34        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       14.07         2.63        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        60.30        16.93        44.75        39.32         4.96 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.01         0.43         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        5.46        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
       10.65        13.91         0.39         0.39        29.95        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       12.43        18.25        21.90        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
       35.90        23.57        26.83        11.77        52.67        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       43.10        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       43.99        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       40.01        22.98         4.04         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 
       54.08         4.01        49.05        12.07        12.33         9.67 
TCGA-85-6560 TCGA-85-6561 
       41.39        40.24 

  HRAS MUTATED HRAS WILD-TYPE 
         21.01           0.39 
  HRAS MUTATED HRAS WILD-TYPE 
         61.61         173.82 
  HRAS MUTATED HRAS WILD-TYPE 
        33.930         22.995 
[1] "21.0 - 61.6 (33.9)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.4"
D18V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  HRAS MUTATED          1        2         0         1          0          0
  HRAS WILD-TYPE       28       68        13        25         24         11
                vv
clus             STAGE IV
  HRAS MUTATED          1
  HRAS WILD-TYPE        2
D18V3, multiclass
            clus
vv           HRAS MUTATED HRAS WILD-TYPE
  STAGE IA              1             28
  STAGE IB              2             68
  STAGE IIA             0             13
  STAGE IIB             1             25
  STAGE IIIA            0             24
  STAGE IIIB            0             11
  STAGE IV              1              2
[1] 7 2
[1] 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
  HRAS MUTATED     1   3   0   1
  HRAS WILD-TYPE  36 112  14  11
D18V4, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T1            1             36
  T2            3            112
  T3            0             14
  T4            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HRAS MUTATED     3   2   0   0
  HRAS WILD-TYPE 113  37  17   5
D18V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0            3            113
  N1            2             37
  N2            0             17
  N3            0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                cls
clus               0   1
  HRAS MUTATED     4   1
  HRAS WILD-TYPE 161   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      4    1
  HRAS WILD-TYPE  161    2
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            4            161
  1            1              2
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  HRAS MUTATED     2   3
  HRAS WILD-TYPE  45 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      2    3
  HRAS WILD-TYPE   45  128
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            2             45
  MALE              3            128
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus               0   1
  HRAS MUTATED     5   0
  HRAS WILD-TYPE 115  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      5    0
  HRAS WILD-TYPE  115   20
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             5            115
  YES            0             20
[1] 2 2
[1] FALSE
D18V9, continuous
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             1             58 
    TCGA-18-3406     TCGA-18-3407     TCGA-18-3410     TCGA-18-4083 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5472     TCGA-33-4533     TCGA-60-2711     TCGA-60-2712 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2715     TCGA-60-2721     TCGA-18-3408     TCGA-18-3412 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-1081     TCGA-21-5782     TCGA-21-5787     TCGA-22-4591 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4595     TCGA-22-4599     TCGA-22-4601 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-4604     TCGA-22-4613     TCGA-22-5473     TCGA-22-5474 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5477     TCGA-22-5478     TCGA-22-5480     TCGA-22-5482 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5485     TCGA-22-5489     TCGA-22-5491     TCGA-22-5492 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-33-4538     TCGA-33-4547     TCGA-33-4582     TCGA-33-4583 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-33-4586     TCGA-34-5234     TCGA-37-4133     TCGA-37-4135 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-37-5819     TCGA-43-3394     TCGA-43-6143     TCGA-43-6647 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6770     TCGA-46-3768     TCGA-60-2698     TCGA-60-2710 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2713     TCGA-60-2719     TCGA-60-2723     TCGA-60-2725 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5131     TCGA-70-6722     TCGA-70-6723 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  HRAS MUTATED                                       1
  HRAS WILD-TYPE                                     4
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  HRAS MUTATED                                        0
  HRAS WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HRAS MUTATED                                                             4
  HRAS WILD-TYPE                                                         168
D18V10, multiclass
                                                             clus
vv                                                            HRAS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
                                                             clus
vv                                                            HRAS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
                vv
clus              R0  R1  R2  RX
  HRAS MUTATED     4   0   0   0
  HRAS WILD-TYPE 143   2   4  10
D18V13, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            4            143
  R1            0              2
  R2            0              4
  RX            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       1                         0     3
  HRAS WILD-TYPE     4                         9   110
D18V14, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                3            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                cls
clus              0  1
  HRAS MUTATED    0  4
  HRAS WILD-TYPE  3 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0    4
  HRAS WILD-TYPE    3   97
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4             97
[1] 2 2
[1] FALSE

Clustering(19) Variable = PI16 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2             0  1
  PI16 MUTATED    3  4
  PI16 WILD-TYPE 87 81
  PI16 MUTATED PI16 WILD-TYPE 
             7            168 
  PI16 MUTATED PI16 WILD-TYPE 
             4             81 
$`PI16 MUTATED`
TCGA-21-1077 TCGA-22-4613 TCGA-22-5485 TCGA-22-5491 TCGA-39-5016 TCGA-60-2725 
       34.78        11.77        30.12        56.32       126.58        26.83 
TCGA-66-2785 
        1.97 

$`PI16 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       27.19        60.66        64.93       129.01       133.74        19.76 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.88        22.49        18.38        41.42         9.01        35.34 
TCGA-60-2721 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       32.32        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
      119.54        46.88        60.89        15.58         9.34        31.63 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
       41.69        33.93        10.82         7.33         4.31         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
       14.10        27.02        20.48        35.08        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       34.75        13.12        19.30        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 
        0.79        71.34        11.74        62.86        16.64        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 
       79.53       173.82       103.53       151.27        14.07         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.01         0.43         7.82         6.81         0.39         3.39 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33         1.94        60.53        68.38        71.18        55.56 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       39.12        33.11        22.98        24.89        21.47         5.46 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       13.32        12.16        13.02         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 
       13.91         0.39         0.39        29.95        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       18.25        21.90        10.22        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       66.54        56.91        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       23.57        11.77        52.67        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        0.99         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        12.00        24.95        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-70-6722 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       49.05        12.07        12.33         9.67        41.39        40.24 

  PI16 MUTATED PI16 WILD-TYPE 
          1.97           0.39 
  PI16 MUTATED PI16 WILD-TYPE 
        126.58         173.82 
  PI16 MUTATED PI16 WILD-TYPE 
        30.120         22.995 
[1] "2.0 - 126.6 (30.1)" "0.4 - 173.8 (23.0)"
[1] "hr=" "1.1"
D19V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  PI16 MUTATED          3        2         1         1          0          0
  PI16 WILD-TYPE       26       68        12        25         24         11
                vv
clus             STAGE IV
  PI16 MUTATED          0
  PI16 WILD-TYPE        3
D19V3, multiclass
            clus
vv           PI16 MUTATED PI16 WILD-TYPE
  STAGE IA              3             26
  STAGE IB              2             68
  STAGE IIA             1             12
  STAGE IIB             1             25
  STAGE IIIA            0             24
  STAGE IIIB            0             11
  STAGE IV              0              3
[1] 7 2
[1] 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
  PI16 MUTATED     3   4   0   0
  PI16 WILD-TYPE  34 111  14  12
D19V4, multiclass
    clus
vv   PI16 MUTATED PI16 WILD-TYPE
  T1            3             34
  T2            4            111
  T3            0             14
  T4            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PI16 MUTATED     5   2   0   0
  PI16 WILD-TYPE 111  37  17   5
D19V5, multiclass
    clus
vv   PI16 MUTATED PI16 WILD-TYPE
  N0            5            111
  N1            2             37
  N2            0             17
  N3            0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                cls
clus               0   1
  PI16 MUTATED     7   0
  PI16 WILD-TYPE 158   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      7    0
  PI16 WILD-TYPE  158    3
   clus
vv  PI16 MUTATED PI16 WILD-TYPE
  0            7            158
  1            0              3
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus               0   1
  PI16 MUTATED     2   5
  PI16 WILD-TYPE  45 126
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      2    5
  PI16 WILD-TYPE   45  126
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  FEMALE            2             45
  MALE              5            126
[1] 2 2
[1] FALSE
D19V8, binary
                cls
clus               0   1
  PI16 MUTATED     5   0
  PI16 WILD-TYPE 115  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      5    0
  PI16 WILD-TYPE  115   20
     clus
vv    PI16 MUTATED PI16 WILD-TYPE
  NO             5            115
  YES            0             20
[1] 2 2
[1] FALSE
D19V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  PI16 MUTATED                                       1
  PI16 WILD-TYPE                                     4
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  PI16 MUTATED                                        0
  PI16 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PI16 MUTATED                                                             6
  PI16 WILD-TYPE                                                         166
D19V10, multiclass
                                                             clus
vv                                                            PI16 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
                                                             clus
vv                                                            PI16 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
D19V12, continuous
[1] "Remove cluster labels:" "PI16 MUTATED"          
clus
  PI16 MUTATED PI16 WILD-TYPE 
             2            104 
    TCGA-18-3406     TCGA-22-5472     TCGA-33-4533     TCGA-39-5039 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-2578     TCGA-60-2711     TCGA-60-2712     TCGA-60-2715 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-60-2721     TCGA-18-3417     TCGA-21-1078     TCGA-21-5782 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-21-5786     TCGA-21-5787     TCGA-22-0944     TCGA-22-1002 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-1011     TCGA-22-1012     TCGA-22-1016     TCGA-22-4591 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4607     TCGA-22-5473     TCGA-22-5474 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5480     TCGA-22-5482     TCGA-22-5492     TCGA-33-4547 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-33-4582     TCGA-33-4583     TCGA-33-4586     TCGA-34-5234 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-34-5240     TCGA-34-5241     TCGA-37-4133     TCGA-37-4135 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-37-5819     TCGA-39-5021     TCGA-39-5022     TCGA-39-5024 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-39-5027     TCGA-39-5028     TCGA-39-5029     TCGA-39-5030 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-39-5031     TCGA-39-5035     TCGA-39-5036     TCGA-39-5037 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-3394     TCGA-43-3920     TCGA-43-6143     TCGA-43-6647 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-56-1622     TCGA-56-5898 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-56-6545     TCGA-56-6546     TCGA-60-2707     TCGA-60-2708 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-60-2709     TCGA-60-2710     TCGA-60-2713     TCGA-60-2719 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-60-2720     TCGA-60-2723     TCGA-60-2724     TCGA-60-2726 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-63-6202     TCGA-66-2727     TCGA-66-2734     TCGA-66-2742 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2744     TCGA-66-2754     TCGA-66-2755     TCGA-66-2756 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2757     TCGA-66-2758     TCGA-66-2759     TCGA-66-2763 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2765     TCGA-66-2766     TCGA-66-2767     TCGA-66-2770 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2771     TCGA-66-2773     TCGA-66-2777     TCGA-66-2778 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2780     TCGA-66-2781     TCGA-66-2782     TCGA-66-2783 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2786     TCGA-66-2787     TCGA-66-2788     TCGA-66-2789 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2791     TCGA-66-2792     TCGA-66-2793     TCGA-66-2794 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-66-2795     TCGA-66-2800     TCGA-85-6560     TCGA-85-6561 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  PI16 MUTATED     7   0   0   0
  PI16 WILD-TYPE 140   2   4  10
D19V13, multiclass
    clus
vv   PI16 MUTATED PI16 WILD-TYPE
  R0            7            140
  R1            0              2
  R2            0              4
  RX            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PI16 MUTATED       0                         0     6
  PI16 WILD-TYPE     5                         9   107
D19V14, multiclass
                           clus
vv                          PI16 MUTATED PI16 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                6            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                cls
clus              0  1
  PI16 MUTATED    0  2
  PI16 WILD-TYPE  3 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      0    2
  PI16 WILD-TYPE    3   99
                        clus
vv                       PI16 MUTATED PI16 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            2             99
[1] 2 2
[1] FALSE
