[1] "ofn"        "-oTCHOL-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/CHOL-TP/15076818/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/15866308/transformed.cor.cli.txt"

nPatients in clinical file=36, in cluster file=35, common to both=35
[1] "Reduce the number of clustering variables from 17 to 16."
[1] 16 35
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             8             27 
  BAP1 MUTATED BAP1 WILD-TYPE 
             8             27 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              5              30 
  HLA-B MUTATED HLA-B WILD-TYPE 
              5              30 
[1] "FTH1 MUTATION ANALYSIS"
[1] 3
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               30 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               30 
[1] "DDHD1 MUTATION ANALYSIS"
[1] 3
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              4              31 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              4              31 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
[1] "MUC21 MUTATION ANALYSIS"
[1] 3
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              4              31 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              4              31 
[1] "OTOP1 MUTATION ANALYSIS"
[1] 3
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              31 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              31 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              30 
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              30 
[1] "FAM35A MUTATION ANALYSIS"
[1] 3
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               32 
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               32 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 35 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "32"                  
freq.contrast "32"               "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 35 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
[7] "RACE"                 
YEARS_TO_BIRTH, nv=28, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
19 12  4 
[1] "table(vv)"
vv
T1 T2 T3 
19 12  4 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
19 12  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
19 12  4 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BAP1 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED    4  4
  BAP1 WILD-TYPE 14 13
  BAP1 MUTATED BAP1 WILD-TYPE 
             8             27 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4             13 
$`BAP1 MUTATED`
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2W TCGA-W5-AA31 TCGA-W5-AA39 
       10.16        20.02         6.77        30.38         0.33         5.59 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
       23.05        24.36 

$`BAP1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        14.63        13.22        23.31        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
        8.91         5.10        35.47        35.18        18.25        31.69 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 
       18.05         0.69         0.85         5.56        12.66        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45        13.22 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.33           0.69 
  BAP1 MUTATED BAP1 WILD-TYPE 
         30.38          64.96 
  BAP1 MUTATED BAP1 WILD-TYPE 
         15.09          18.05 
[1] "0.3 - 30.4 (15.1)" "0.7 - 65.0 (18.1)"
[1] "hr=" "1.5"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED         4        3         0        0         1         0
  BAP1 WILD-TYPE      15        6         1        1         1         3
D1V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              4             15
  STAGE II             3              6
  STAGE III            0              1
  STAGE IV             0              1
  STAGE IVA            1              1
  STAGE IVB            0              3
[1] 6 2
[1] 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
  BAP1 MUTATED    4  4  0
  BAP1 WILD-TYPE 15  8  4
D1V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            4             15
  T2            4              8
  T3            0              4
[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"
D1V5, binary
                cls
clus              0  1
  BAP1 MUTATED    6  1
  BAP1 WILD-TYPE 19  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      6    1
  BAP1 WILD-TYPE   19    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            6             19
  1            1              4
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  BAP1 MUTATED    8  0
  BAP1 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      8    0
  BAP1 WILD-TYPE   20    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            8             20
  1            0              4
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  BAP1 MUTATED    3  5
  BAP1 WILD-TYPE 16 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3    5
  BAP1 WILD-TYPE   16   11
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            3             16
  MALE              5             11
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED       1                         1     6
  BAP1 WILD-TYPE     2                         1    24
D1V8, multiclass
                           clus
vv                          BAP1 MUTATED BAP1 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            1              1
  WHITE                                6             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = PBRM1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  PBRM1 MUTATED    4  4
  PBRM1 WILD-TYPE 14 13
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              4              13 
$`PBRM1 MUTATED`
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA30 TCGA-W5-AA38 TCGA-W5-AA39 
       20.02         6.77        63.75        35.47        31.69         5.59 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       12.66        24.36 

$`PBRM1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G 
       11.15        14.63        13.22        23.31        10.16        64.96 
TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         8.91         5.10         0.33        35.18        18.25 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       18.05         0.69         0.85         5.56        23.05        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45        13.22 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           5.59            0.33 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          63.75           64.96 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          22.19           17.06 
[1] "5.6 - 63.8 (22.2)" "0.3 - 65.0 (17.1)"
[1] "hr=" "1.3"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  PBRM1 MUTATED         5        2         0        0         1         0
  PBRM1 WILD-TYPE      14        7         1        1         1         3
D2V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I               5              14
  STAGE II              2               7
  STAGE III             0               1
  STAGE IV              0               1
  STAGE IVA             1               1
  STAGE IVB             0               3
[1] 6 2
[1] 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
  PBRM1 MUTATED    5  2  1
  PBRM1 WILD-TYPE 14 10  3
D2V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1             5              14
  T2             2              10
  T3             1               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                 cls
clus               0  1
  PBRM1 MUTATED    7  1
  PBRM1 WILD-TYPE 18  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      7    1
  PBRM1 WILD-TYPE   18    4
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             7              18
  1             1               4
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus               0  1
  PBRM1 MUTATED    8  0
  PBRM1 WILD-TYPE 20  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      8    0
  PBRM1 WILD-TYPE   20    4
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             8              20
  1             0               4
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus               0  1
  PBRM1 MUTATED    3  5
  PBRM1 WILD-TYPE 16 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      3    5
  PBRM1 WILD-TYPE   16   11
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             3              16
  MALE               5              11
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       0                         0     8
  PBRM1 WILD-TYPE     3                         2    22
D2V8, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 8              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MLL3 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  MLL3 MUTATED    5  2
  MLL3 WILD-TYPE 13 15
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
  MLL3 MUTATED MLL3 WILD-TYPE 
             2             15 
$`MLL3 MUTATED`
TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W6-AA0S 
       13.22        64.96        63.75         5.10        35.47        18.05 
TCGA-ZH-A8Y2 
       23.05 

$`MLL3 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
       30.38         8.91         0.33        35.18        18.25        31.69 
TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
        5.59         0.69         0.85         5.56        12.66        24.36 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45        13.22 

  MLL3 MUTATED MLL3 WILD-TYPE 
          5.10           0.33 
  MLL3 MUTATED MLL3 WILD-TYPE 
         64.96          48.82 
  MLL3 MUTATED MLL3 WILD-TYPE 
        23.050         15.845 
[1] "5.1 - 65.0 (23.1)" "0.3 - 48.8 (15.8)"
[1] "hr=" "5.7"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  MLL3 MUTATED         5        1         0        0         0         1
  MLL3 WILD-TYPE      14        8         1        1         2         2
D3V3, multiclass
           clus
vv          MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I              5             14
  STAGE II             1              8
  STAGE III            0              1
  STAGE IV             0              1
  STAGE IVA            0              2
  STAGE IVB            1              2
[1] 6 2
[1] 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
  MLL3 MUTATED    5  1  1
  MLL3 WILD-TYPE 14 11  3
D3V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            5             14
  T2            1             11
  T3            1              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                cls
clus              0  1
  MLL3 MUTATED    5  1
  MLL3 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      5    1
  MLL3 WILD-TYPE   20    4
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0            5             20
  1            1              4
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus              0  1
  MLL3 MUTATED    5  1
  MLL3 WILD-TYPE 23  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      5    1
  MLL3 WILD-TYPE   23    3
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0            5             23
  1            1              3
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus              0  1
  MLL3 MUTATED    5  2
  MLL3 WILD-TYPE 14 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      5    2
  MLL3 WILD-TYPE   14   14
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE            5             14
  MALE              2             14
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED       0                         1     6
  MLL3 WILD-TYPE     3                         1    24
D3V8, multiclass
                           clus
vv                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            1              1
  WHITE                                6             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = TP53 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    3  2
  TP53 WILD-TYPE 15 15
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
  TP53 MUTATED TP53 WILD-TYPE 
             2             15 
$`TP53 MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2I TCGA-W5-AA2O TCGA-ZH-A8Y5 
       13.22        23.31        63.75        21.04        33.37 

$`TP53 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       20.88         1.64        48.82        40.11        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
        8.91         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        23.05        24.36        17.06        13.45        13.22 

  TP53 MUTATED TP53 WILD-TYPE 
         13.22           0.33 
  TP53 MUTATED TP53 WILD-TYPE 
         63.75          64.96 
  TP53 MUTATED TP53 WILD-TYPE 
        23.310         15.845 
[1] "13.2 - 63.8 (23.3)" "0.3 - 65.0 (15.8)" 
[1] "hr=" "2.3"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  TP53 MUTATED         3        0         0        0         0         2
  TP53 WILD-TYPE      16        9         1        1         2         1
D4V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              3             16
  STAGE II             0              9
  STAGE III            0              1
  STAGE IV             0              1
  STAGE IVA            0              2
  STAGE IVB            2              1
[1] 6 2
[1] 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
  TP53 MUTATED    3  0  2
  TP53 WILD-TYPE 16 12  2
D4V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            3             16
  T2            0             12
  T3            2              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                cls
clus              0  1
  TP53 MUTATED    3  2
  TP53 WILD-TYPE 22  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    2
  TP53 WILD-TYPE   22    3
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            3             22
  1            2              3
[1] 2 2
[1] FALSE
D4V6, binary
                cls
clus              0  1
  TP53 MUTATED    3  2
  TP53 WILD-TYPE 25  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    2
  TP53 WILD-TYPE   25    2
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            3             25
  1            2              2
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE 17 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE   17   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            2             17
  MALE              3             13
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0     5
  TP53 WILD-TYPE     3                         2    25
D4V8, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              2
  WHITE                                5             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = HLA-B MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  HLA-B MUTATED    2  3
  HLA-B WILD-TYPE 16 14
  HLA-B MUTATED HLA-B WILD-TYPE 
              5              30 
  HLA-B MUTATED HLA-B WILD-TYPE 
              3              14 
$`HLA-B MUTATED`
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA31 TCGA-YR-A95A TCGA-ZH-A8Y2 
       64.96        21.04         0.33         0.85        23.05 

$`HLA-B WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
        6.77        20.88        63.75         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       20.61        30.38         8.91         5.10        35.47        35.18 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 
       18.25        31.69         5.59        18.05         0.69         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        24.36        33.37        17.06        13.45        13.22 

  HLA-B MUTATED HLA-B WILD-TYPE 
           0.33            0.69 
  HLA-B MUTATED HLA-B WILD-TYPE 
          64.96           63.75 
  HLA-B MUTATED HLA-B WILD-TYPE 
         21.040          17.555 
[1] "0.3 - 65.0 (21.0)" "0.7 - 63.8 (17.6)"
[1] "hr=" "1.1"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  HLA-B MUTATED         4        0         0        1         0         0
  HLA-B WILD-TYPE      15        9         1        0         2         3
D5V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               4              15
  STAGE II              0               9
  STAGE III             0               1
  STAGE IV              1               0
  STAGE IVA             0               2
  STAGE IVB             0               3
[1] 6 2
[1] 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
  HLA-B MUTATED    4  1  0
  HLA-B WILD-TYPE 15 11  4
D5V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             4              15
  T2             1              11
  T3             0               4
[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"
D5V5, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  0
  HLA-B WILD-TYPE 22  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    0
  HLA-B WILD-TYPE   22    5
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             3              22
  1             0               5
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus               0  1
  HLA-B MUTATED    4  1
  HLA-B WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      4    1
  HLA-B WILD-TYPE   24    3
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             4              24
  1             1               3
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus               0  1
  HLA-B MUTATED    2  3
  HLA-B WILD-TYPE 17 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    3
  HLA-B WILD-TYPE   17   13
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             2              17
  MALE               3              13
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       0                         1     4
  HLA-B WILD-TYPE     3                         1    26
D5V8, multiclass
                           clus
vv                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             1               1
  WHITE                                 4              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = FTH1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  FTH1 MUTATED    2  1
  FTH1 WILD-TYPE 16 16
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
  FTH1 MUTATED FTH1 WILD-TYPE 
             1             16 
$`FTH1 MUTATED`
TCGA-4G-AAZT TCGA-W5-AA2W TCGA-W5-AA2Z 
        6.77        30.38         5.10 

$`FTH1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       40.11        20.61         8.91        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       18.25        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        5.56        12.66        23.05        24.36        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45        13.22 

  FTH1 MUTATED FTH1 WILD-TYPE 
          5.10           0.33 
  FTH1 MUTATED FTH1 WILD-TYPE 
         30.38          64.96 
  FTH1 MUTATED FTH1 WILD-TYPE 
          6.77          18.15 
[1] "5.1 - 30.4 (6.8)"  "0.3 - 65.0 (18.1)"
[1] "hr=" "1"  
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  FTH1 MUTATED         1        1         0        0         1         0
  FTH1 WILD-TYPE      18        8         1        1         1         3
D6V3, multiclass
           clus
vv          FTH1 MUTATED FTH1 WILD-TYPE
  STAGE I              1             18
  STAGE II             1              8
  STAGE III            0              1
  STAGE IV             0              1
  STAGE IVA            1              1
  STAGE IVB            0              3
[1] 6 2
[1] 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
  FTH1 MUTATED    1  2  0
  FTH1 WILD-TYPE 18 10  4
D6V4, multiclass
    clus
vv   FTH1 MUTATED FTH1 WILD-TYPE
  T1            1             18
  T2            2             10
  T3            0              4
[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"
D6V5, binary
                cls
clus              0  1
  FTH1 MUTATED    2  1
  FTH1 WILD-TYPE 23  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    1
  FTH1 WILD-TYPE   23    4
   clus
vv  FTH1 MUTATED FTH1 WILD-TYPE
  0            2             23
  1            1              4
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus              0  1
  FTH1 MUTATED    3  0
  FTH1 WILD-TYPE 25  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      3    0
  FTH1 WILD-TYPE   25    4
   clus
vv  FTH1 MUTATED FTH1 WILD-TYPE
  0            3             25
  1            0              4
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus              0  1
  FTH1 MUTATED    2  1
  FTH1 WILD-TYPE 17 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    1
  FTH1 WILD-TYPE   17   15
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  FEMALE            2             17
  MALE              1             15
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FTH1 MUTATED       0                         0     3
  FTH1 WILD-TYPE     3                         2    27
D6V8, multiclass
                           clus
vv                          FTH1 MUTATED FTH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              2
  WHITE                                3             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    2  3
  ARID1A WILD-TYPE 16 14
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               30 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               14 
$`ARID1A MUTATED`
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       20.02         6.77         0.69         0.85         5.56 

$`ARID1A WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G 
       11.15        14.63        13.22        23.31        10.16        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y1 
       35.18        18.25        31.69         5.59        18.05        12.66 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       23.05        24.36        33.37        17.06        13.45        13.22 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.69             0.33 
  ARID1A MUTATED ARID1A WILD-TYPE 
           20.02            64.96 
  ARID1A MUTATED ARID1A WILD-TYPE 
            5.56            19.43 
[1] "0.7 - 20.0 (5.6)"  "0.3 - 65.0 (19.4)"
[1] "hr=" "6"  
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  ARID1A MUTATED         1        3         0        1         0         0
  ARID1A WILD-TYPE      18        6         1        0         2         3
D7V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                1               18
  STAGE II               3                6
  STAGE III              0                1
  STAGE IV               1                0
  STAGE IVA              0                2
  STAGE IVB              0                3
[1] 6 2
[1] 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
  ARID1A MUTATED    1  4  0
  ARID1A WILD-TYPE 18  8  4
D7V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              1               18
  T2              4                8
  T3              0                4
[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"
D7V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  0
  ARID1A WILD-TYPE 22  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    0
  ARID1A WILD-TYPE   22    5
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              3               22
  1              0                5
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  1
  ARID1A WILD-TYPE 25  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    1
  ARID1A WILD-TYPE   25    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              3               25
  1              1                3
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  2
  ARID1A WILD-TYPE 16 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    2
  ARID1A WILD-TYPE   16   14
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              3               16
  MALE                2               14
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       1                         0     4
  ARID1A WILD-TYPE     2                         2    26
D7V8, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                2
  WHITE                                  4               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = DDHD1 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  DDHD1 MUTATED    3  1
  DDHD1 WILD-TYPE 15 16
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              4              31 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              1              16 
$`DDHD1 MUTATED`
TCGA-4G-AAZO TCGA-W5-AA2O TCGA-W5-AA2Z TCGA-W5-AA33 
       20.02        21.04         5.10        35.18 

$`DDHD1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        10.16         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       64.96        20.88        63.75         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA34 
       20.61        30.38         8.91        35.47         0.33        18.25 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       12.66        23.05        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

  DDHD1 MUTATED DDHD1 WILD-TYPE 
           5.10            0.33 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          35.18           64.96 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          20.53           17.06 
[1] "5.1 - 35.2 (20.5)" "0.3 - 65.0 (17.1)"
[1] "hr=" "2"  
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  DDHD1 MUTATED         2        2         0        0         0         0
  DDHD1 WILD-TYPE      17        7         1        1         2         3
D8V3, multiclass
           clus
vv          DDHD1 MUTATED DDHD1 WILD-TYPE
  STAGE I               2              17
  STAGE II              2               7
  STAGE III             0               1
  STAGE IV              0               1
  STAGE IVA             0               2
  STAGE IVB             0               3
[1] 6 2
[1] 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
  DDHD1 MUTATED    2  2  0
  DDHD1 WILD-TYPE 17 10  4
D8V4, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  T1             2              17
  T2             2              10
  T3             0               4
[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"
D8V5, binary
                 cls
clus               0  1
  DDHD1 MUTATED    4  0
  DDHD1 WILD-TYPE 21  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      4    0
  DDHD1 WILD-TYPE   21    5
   clus
vv  DDHD1 MUTATED DDHD1 WILD-TYPE
  0             4              21
  1             0               5
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus               0  1
  DDHD1 MUTATED    4  0
  DDHD1 WILD-TYPE 24  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      4    0
  DDHD1 WILD-TYPE   24    4
   clus
vv  DDHD1 MUTATED DDHD1 WILD-TYPE
  0             4              24
  1             0               4
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus               0  1
  DDHD1 MUTATED    2  2
  DDHD1 WILD-TYPE 17 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      2    2
  DDHD1 WILD-TYPE   17   14
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  FEMALE             2              17
  MALE               2              14
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDHD1 MUTATED       0                         0     4
  DDHD1 WILD-TYPE     3                         2    26
D8V8, multiclass
                           clus
vv                          DDHD1 MUTATED DDHD1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 4              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = IDH1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  IDH1 MUTATED    1  3
  IDH1 WILD-TYPE 17 14
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
  IDH1 MUTATED IDH1 WILD-TYPE 
             3             14 
$`IDH1 MUTATED`
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA34 TCGA-YR-A95A 
       64.96        21.04        18.25         0.85 

$`IDH1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
        6.77        20.88        63.75         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 
       35.18        31.69         5.59        18.05         0.69         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       12.66        23.05        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.85           0.33 
  IDH1 MUTATED IDH1 WILD-TYPE 
         64.96          63.75 
  IDH1 MUTATED IDH1 WILD-TYPE 
        19.645         17.060 
[1] "0.8 - 65.0 (19.6)" "0.3 - 63.8 (17.1)"
[1] "hr=" "1.2"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  IDH1 MUTATED         3        0         0        1         0         0
  IDH1 WILD-TYPE      16        9         1        0         2         3
D9V3, multiclass
           clus
vv          IDH1 MUTATED IDH1 WILD-TYPE
  STAGE I              3             16
  STAGE II             0              9
  STAGE III            0              1
  STAGE IV             1              0
  STAGE IVA            0              2
  STAGE IVB            0              3
[1] 6 2
[1] 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
  IDH1 MUTATED    3  1  0
  IDH1 WILD-TYPE 16 11  4
D9V4, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T1            3             16
  T2            1             11
  T3            0              4
[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"
D9V5, binary
                cls
clus              0  1
  IDH1 MUTATED    3  0
  IDH1 WILD-TYPE 22  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3    0
  IDH1 WILD-TYPE   22    5
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            3             22
  1            0              5
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus              0  1
  IDH1 MUTATED    3  1
  IDH1 WILD-TYPE 25  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3    1
  IDH1 WILD-TYPE   25    3
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            3             25
  1            1              3
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus              0  1
  IDH1 MUTATED    2  2
  IDH1 WILD-TYPE 17 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      2    2
  IDH1 WILD-TYPE   17   14
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            2             17
  MALE              2             14
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0     4
  IDH1 WILD-TYPE     3                         2    26
D9V8, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              2
  WHITE                                4             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MUC2 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  MUC2 MUTATED    2  5
  MUC2 WILD-TYPE 16 12
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
  MUC2 MUTATED MUC2 WILD-TYPE 
             5             12 
$`MUC2 MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2H TCGA-W5-AA2O TCGA-ZD-A8I3 TCGA-ZH-A8Y4 
       11.15        13.22        20.88        21.04         5.56        24.36 
TCGA-ZU-A8S4 
       13.22 

$`MUC2 WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        10.16        20.02         6.77        64.96 
TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       63.75         1.64        48.82        40.11        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
        8.91         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 
       31.69         5.59        18.05         0.69         0.85        12.66 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       23.05        33.37        17.06        13.45 

  MUC2 MUTATED MUC2 WILD-TYPE 
          5.56           0.33 
  MUC2 MUTATED MUC2 WILD-TYPE 
         24.36          64.96 
  MUC2 MUTATED MUC2 WILD-TYPE 
         13.22          18.15 
[1] "5.6 - 24.4 (13.2)" "0.3 - 65.0 (18.1)"
[1] "hr=" "2.5"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  MUC2 MUTATED         4        1         1        0         0         1
  MUC2 WILD-TYPE      15        8         0        1         2         2
D10V3, multiclass
           clus
vv          MUC2 MUTATED MUC2 WILD-TYPE
  STAGE I              4             15
  STAGE II             1              8
  STAGE III            1              0
  STAGE IV             0              1
  STAGE IVA            0              2
  STAGE IVB            1              2
[1] 6 2
[1] 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
  MUC2 MUTATED    4  1  2
  MUC2 WILD-TYPE 15 11  2
D10V4, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  T1            4             15
  T2            1             11
  T3            2              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                cls
clus              0  1
  MUC2 MUTATED    5  1
  MUC2 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      5    1
  MUC2 WILD-TYPE   20    4
   clus
vv  MUC2 MUTATED MUC2 WILD-TYPE
  0            5             20
  1            1              4
[1] 2 2
[1] FALSE
D10V6, binary
                cls
clus              0  1
  MUC2 MUTATED    5  1
  MUC2 WILD-TYPE 23  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      5    1
  MUC2 WILD-TYPE   23    3
   clus
vv  MUC2 MUTATED MUC2 WILD-TYPE
  0            5             23
  1            1              3
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus              0  1
  MUC2 MUTATED    3  4
  MUC2 WILD-TYPE 16 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      3    4
  MUC2 WILD-TYPE   16   12
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  FEMALE            3             16
  MALE              4             12
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC2 MUTATED       2                         0     5
  MUC2 WILD-TYPE     1                         2    25
D10V8, multiclass
                           clus
vv                          MUC2 MUTATED MUC2 WILD-TYPE
  ASIAN                                2              1
  BLACK OR AFRICAN AMERICAN            0              2
  WHITE                                5             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MUC21 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  MUC21 MUTATED    1  2
  MUC21 WILD-TYPE 17 15
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
  MUC21 MUTATED MUC21 WILD-TYPE 
              2              15 
$`MUC21 MUTATED`
TCGA-3X-AAV9 TCGA-4G-AAZT TCGA-ZU-A8S4 
       11.15         6.77        13.22 

$`MUC21 WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       14.63        13.22        23.31        10.16        20.02        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       35.18        18.25        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.85         5.56        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       17.06        13.45 

  MUC21 MUTATED MUC21 WILD-TYPE 
           6.77            0.33 
  MUC21 MUTATED MUC21 WILD-TYPE 
          13.22           64.96 
  MUC21 MUTATED MUC21 WILD-TYPE 
         11.150          19.135 
[1] "6.8 - 13.2 (11.2)" "0.3 - 65.0 (19.1)"
[1] "hr=" "4"  
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  MUC21 MUTATED         3        0         0        0         0         0
  MUC21 WILD-TYPE      16        9         1        1         2         3
D11V3, multiclass
           clus
vv          MUC21 MUTATED MUC21 WILD-TYPE
  STAGE I               3              16
  STAGE II              0               9
  STAGE III             0               1
  STAGE IV              0               1
  STAGE IVA             0               2
  STAGE IVB             0               3
[1] 6 2
[1] 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
  MUC21 MUTATED    3  0  0
  MUC21 WILD-TYPE 16 12  4
D11V4, multiclass
    clus
vv   MUC21 MUTATED MUC21 WILD-TYPE
  T1             3              16
  T2             0              12
  T3             0               4
[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"
D11V5, binary
                 cls
clus               0  1
  MUC21 MUTATED    2  0
  MUC21 WILD-TYPE 23  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      2    0
  MUC21 WILD-TYPE   23    5
   clus
vv  MUC21 MUTATED MUC21 WILD-TYPE
  0             2              23
  1             0               5
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus               0  1
  MUC21 MUTATED    2  0
  MUC21 WILD-TYPE 26  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      2    0
  MUC21 WILD-TYPE   26    4
   clus
vv  MUC21 MUTATED MUC21 WILD-TYPE
  0             2              26
  1             0               4
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus               0  1
  MUC21 MUTATED    0  3
  MUC21 WILD-TYPE 19 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      0    3
  MUC21 WILD-TYPE   19   13
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  FEMALE             0              19
  MALE               3              13
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC21 MUTATED       1                         0     2
  MUC21 WILD-TYPE     2                         2    28
D11V8, multiclass
                           clus
vv                          MUC21 MUTATED MUC21 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 2              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = PAXIP1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2               0  1
  PAXIP1 MUTATED    1  3
  PAXIP1 WILD-TYPE 17 14
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               3               14 
$`PAXIP1 MUTATED`
TCGA-W5-AA2G TCGA-W5-AA2W TCGA-W5-AA2X TCGA-ZH-A8Y4 
       64.96        30.38         8.91        24.36 

$`PAXIP1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
        6.77        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       40.11        20.61         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       18.25        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        5.56        12.66        23.05        33.37        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            8.91             0.33 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
           64.96            63.75 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
           27.37            17.06 
[1] "8.9 - 65.0 (27.4)" "0.3 - 63.8 (17.1)"
[1] "hr=" "1.1"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  PAXIP1 MUTATED         2        0         0        0         1         1
  PAXIP1 WILD-TYPE      17        9         1        1         1         2
D12V3, multiclass
           clus
vv          PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                2               17
  STAGE II               0                9
  STAGE III              0                1
  STAGE IV               0                1
  STAGE IVA              1                1
  STAGE IVB              1                2
[1] 6 2
[1] 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
  PAXIP1 MUTATED    2  2  0
  PAXIP1 WILD-TYPE 17 10  4
D12V4, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T1              2               17
  T2              2               10
  T3              0                4
[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"
D12V5, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    2  2
  PAXIP1 WILD-TYPE 23  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      2    2
  PAXIP1 WILD-TYPE   23    3
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0              2               23
  1              2                3
[1] 2 2
[1] FALSE
D12V6, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    3  1
  PAXIP1 WILD-TYPE 25  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      3    1
  PAXIP1 WILD-TYPE   25    3
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0              3               25
  1              1                3
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    2  2
  PAXIP1 WILD-TYPE 17 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      2    2
  PAXIP1 WILD-TYPE   17   14
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  FEMALE              2               17
  MALE                2               14
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAXIP1 MUTATED       0                         0     4
  PAXIP1 WILD-TYPE     3                         2    26
D12V8, multiclass
                           clus
vv                          PAXIP1 MUTATED PAXIP1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                2
  WHITE                                  4               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = EPHA2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  EPHA2 MUTATED    1  3
  EPHA2 WILD-TYPE 17 14
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              4              31 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              3              14 
$`EPHA2 MUTATED`
TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2I TCGA-YR-A95A 
       14.63        64.96        63.75         0.85 

$`EPHA2 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        13.22        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       30.38         8.91         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 
       18.25        31.69         5.59        18.05         0.69         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       12.66        23.05        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           0.85            0.33 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          64.96           48.82 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          39.19           18.05 
[1] "0.8 - 65.0 (39.2)" "0.3 - 48.8 (18.1)"
[1] "hr=" "1.4"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  EPHA2 MUTATED         2        1         0        1         0         0
  EPHA2 WILD-TYPE      17        8         1        0         2         3
D13V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               2              17
  STAGE II              1               8
  STAGE III             0               1
  STAGE IV              1               0
  STAGE IVA             0               2
  STAGE IVB             0               3
[1] 6 2
[1] 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
  EPHA2 MUTATED    2  2  0
  EPHA2 WILD-TYPE 17 10  4
D13V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             2              17
  T2             2              10
  T3             0               4
[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"
D13V5, binary
                 cls
clus               0  1
  EPHA2 MUTATED    2  0
  EPHA2 WILD-TYPE 23  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      2    0
  EPHA2 WILD-TYPE   23    5
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             2              23
  1             0               5
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus               0  1
  EPHA2 MUTATED    3  1
  EPHA2 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      3    1
  EPHA2 WILD-TYPE   25    3
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             3              25
  1             1               3
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus               0  1
  EPHA2 MUTATED    2  2
  EPHA2 WILD-TYPE 17 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      2    2
  EPHA2 WILD-TYPE   17   14
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             2              17
  MALE               2              14
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED       0                         0     4
  EPHA2 WILD-TYPE     3                         2    26
D13V8, multiclass
                           clus
vv                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 4              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = OTOP1 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  OTOP1 MUTATED    1  3
  OTOP1 WILD-TYPE 17 14
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              31 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              3              14 
$`OTOP1 MUTATED`
TCGA-W5-AA2R TCGA-W5-AA34 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       48.82        18.25        12.66        24.36 

$`OTOP1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
        0.33        35.18        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        0.85         5.56        23.05        33.37        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

  OTOP1 MUTATED OTOP1 WILD-TYPE 
          12.66            0.33 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
          48.82           64.96 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
         21.305          17.060 
[1] "12.7 - 48.8 (21.3)" "0.3 - 65.0 (17.1)" 
[1] "hr=" "1.3"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  OTOP1 MUTATED         3        0         0        0         1         0
  OTOP1 WILD-TYPE      16        9         1        1         1         3
D14V3, multiclass
           clus
vv          OTOP1 MUTATED OTOP1 WILD-TYPE
  STAGE I               3              16
  STAGE II              0               9
  STAGE III             0               1
  STAGE IV              0               1
  STAGE IVA             1               1
  STAGE IVB             0               3
[1] 6 2
[1] 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
  OTOP1 MUTATED    3  0  1
  OTOP1 WILD-TYPE 16 12  3
D14V4, multiclass
    clus
vv   OTOP1 MUTATED OTOP1 WILD-TYPE
  T1             3              16
  T2             0              12
  T3             1               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                 cls
clus               0  1
  OTOP1 MUTATED    3  1
  OTOP1 WILD-TYPE 22  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      3    1
  OTOP1 WILD-TYPE   22    4
   clus
vv  OTOP1 MUTATED OTOP1 WILD-TYPE
  0             3              22
  1             1               4
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus               0  1
  OTOP1 MUTATED    4  0
  OTOP1 WILD-TYPE 24  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      4    0
  OTOP1 WILD-TYPE   24    4
   clus
vv  OTOP1 MUTATED OTOP1 WILD-TYPE
  0             4              24
  1             0               4
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus               0  1
  OTOP1 MUTATED    3  1
  OTOP1 WILD-TYPE 16 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      3    1
  OTOP1 WILD-TYPE   16   15
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  FEMALE             3              16
  MALE               1              15
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTOP1 MUTATED       0                         0     4
  OTOP1 WILD-TYPE     3                         2    26
D14V8, multiclass
                           clus
vv                          OTOP1 MUTATED OTOP1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 4              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = CDC27 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    1  4
  CDC27 WILD-TYPE 17 13
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              30 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              13 
$`CDC27 MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2W TCGA-W5-AA31 TCGA-W5-AA34 TCGA-YR-A95A 
       11.15        30.38         0.33        18.25         0.85 

$`CDC27 WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       14.63        13.22        23.31        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       40.11        20.61         8.91         5.10        35.47        35.18 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y1 
       31.69         5.59        18.05         0.69         5.56        12.66 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       23.05        24.36        33.37        17.06        13.45        13.22 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.33            0.69 
  CDC27 MUTATED CDC27 WILD-TYPE 
          30.38           64.96 
  CDC27 MUTATED CDC27 WILD-TYPE 
         11.150          19.035 
[1] "0.3 - 30.4 (11.2)" "0.7 - 65.0 (19.0)"
[1] "hr=" "3.3"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  CDC27 MUTATED         3        0         0        1         1         0
  CDC27 WILD-TYPE      16        9         1        0         1         3
D15V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I               3              16
  STAGE II              0               9
  STAGE III             0               1
  STAGE IV              1               0
  STAGE IVA             1               1
  STAGE IVB             0               3
[1] 6 2
[1] 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
  CDC27 MUTATED    3  2  0
  CDC27 WILD-TYPE 16 10  4
D15V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             3              16
  T2             2              10
  T3             0               4
[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"
D15V5, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE 22  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    1
  CDC27 WILD-TYPE   22    4
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             3              22
  1             1               4
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    4  1
  CDC27 WILD-TYPE 24  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      4    1
  CDC27 WILD-TYPE   24    3
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             4              24
  1             1               3
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  3
  CDC27 WILD-TYPE 17 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    3
  CDC27 WILD-TYPE   17   13
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             2              17
  MALE               3              13
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       1                         0     4
  CDC27 WILD-TYPE     2                         2    26
D15V8, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               2
  WHITE                                 4              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = FAM35A MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  FAM35A MUTATED    0  3
  FAM35A WILD-TYPE 18 14
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               32 
  FAM35A MUTATED FAM35A WILD-TYPE 
               3               14 
$`FAM35A MUTATED`
TCGA-W5-AA2X TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        8.91        23.05        24.36 

$`FAM35A WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        40.11        20.61        30.38         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
        0.33        35.18        18.25        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.69         0.85         5.56        12.66        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45        13.22 

  FAM35A MUTATED FAM35A WILD-TYPE 
            8.91             0.33 
  FAM35A MUTATED FAM35A WILD-TYPE 
           24.36            64.96 
  FAM35A MUTATED FAM35A WILD-TYPE 
          23.050           17.555 
[1] "8.9 - 24.4 (23.1)" "0.3 - 65.0 (17.6)"
[1] "hr=" "2.3"
D16V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  FAM35A MUTATED         2        0         0        0         0         1
  FAM35A WILD-TYPE      17        9         1        1         2         2
D16V3, multiclass
           clus
vv          FAM35A MUTATED FAM35A WILD-TYPE
  STAGE I                2               17
  STAGE II               0                9
  STAGE III              0                1
  STAGE IV               0                1
  STAGE IVA              0                2
  STAGE IVB              1                2
[1] 6 2
[1] 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
  FAM35A MUTATED    2  1  0
  FAM35A WILD-TYPE 17 11  4
D16V4, multiclass
    clus
vv   FAM35A MUTATED FAM35A WILD-TYPE
  T1              2               17
  T2              1               11
  T3              0                4
[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"
D16V5, binary
                  cls
clus                0  1
  FAM35A MUTATED    1  1
  FAM35A WILD-TYPE 24  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM35A MUTATED      1    1
  FAM35A WILD-TYPE   24    4
   clus
vv  FAM35A MUTATED FAM35A WILD-TYPE
  0              1               24
  1              1                4
[1] 2 2
[1] FALSE
D16V6, binary
                  cls
clus                0  1
  FAM35A MUTATED    2  1
  FAM35A WILD-TYPE 26  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM35A MUTATED      2    1
  FAM35A WILD-TYPE   26    3
   clus
vv  FAM35A MUTATED FAM35A WILD-TYPE
  0              2               26
  1              1                3
[1] 2 2
[1] FALSE
D16V7, binary
                  cls
clus                0  1
  FAM35A MUTATED    1  2
  FAM35A WILD-TYPE 18 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM35A MUTATED      1    2
  FAM35A WILD-TYPE   18   14
        clus
vv       FAM35A MUTATED FAM35A WILD-TYPE
  FEMALE              1               18
  MALE                2               14
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM35A MUTATED       0                         1     2
  FAM35A WILD-TYPE     3                         1    28
D16V8, multiclass
                           clus
vv                          FAM35A MUTATED FAM35A WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              1                1
  WHITE                                  2               28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
