[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/22489349/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22563789/transformed.cor.cli.txt"

nPatients in clinical file=45, in cluster file=35, common to both=35
[1] "Reduce the number of clustering variables from 17 to 15."
[1] 15 35
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              8              27 
[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] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
  MLL3 MUTATED MLL3 WILD-TYPE 
             7             28 
[1] "FTH1 MUTATION ANALYSIS"
[1] 3
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             32 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
  TP53 MUTATED TP53 WILD-TYPE 
             5             30 
[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] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             28 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             31 
[1] "MUC21 MUTATION ANALYSIS"
[1] 3
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
  MUC21 MUTATED MUC21 WILD-TYPE 
              3              32 
[1] "CLIP4 MUTATION ANALYSIS"
[1] 3
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              4              31 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              4              31 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
             6             29 
  BAP1 MUTATED BAP1 WILD-TYPE 
             6             29 
[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] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               31 
[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] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "RACE"                                
[16] "ETHNICITY"                           

Input Data has 16 rows and 35 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=27,	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=18,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'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 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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"               
[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 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
[4] "PATHOLOGY_N_STAGE" "PATHOLOGY_M_STAGE" "GENDER"           
[7] "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"    "RACE"             
YEARS_TO_BIRTH, nv=27, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PBRM1 MUTATION ANALYSIS
D1V1, 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-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA30 
       12.66        24.36        38.70        13.81        63.75        37.91 
TCGA-W5-AA38 TCGA-W5-AA39 
       48.36         5.59 

$`PBRM1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       11.15        13.22        40.11         0.33        19.79        14.63 
TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q 
       23.31        21.37        64.96        35.41        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 
       50.70        20.61        30.38         8.91        53.06        47.64 
TCGA-W5-AA34 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       18.25        26.56         0.69         0.85         5.56        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       40.41        17.06         3.22 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           5.59            0.33 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          63.75           64.96 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         31.135          20.610 
[1] "5.6 - 63.8 (31.1)" "0.3 - 65.0 (20.6)"
[1] "hr=" "1.3"
D1V2, 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
D1V3, 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
D1V4, 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"
D1V5, 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
D1V6, 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
D1V7, 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              CHOLANGIOCARCINOMA; DISTAL
  PBRM1 MUTATED                            0
  PBRM1 WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  PBRM1 MUTATED                                     0
  PBRM1 WILD-TYPE                                   3
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  PBRM1 MUTATED                                  8
  PBRM1 WILD-TYPE                               22
D1V8, multiclass
                                     clus
vv                                    PBRM1 MUTATED PBRM1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             0               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  PBRM1 MUTATED    4  3  1
  PBRM1 WILD-TYPE 23  2  2
D1V9, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0             4              23
  R1             3               2
  RX             1               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       0                         0     8
  PBRM1 WILD-TYPE     3                         2    22
D1V10, 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(2) Variable = HLA-B MUTATION ANALYSIS
D2V1, 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-AA31 TCGA-W5-AA2G TCGA-W5-AA2O TCGA-YR-A95A TCGA-ZH-A8Y2 
        0.33        64.96        21.04         0.85        23.05 

$`HLA-B WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        13.22        40.11        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H 
       14.63        23.31        21.37        38.70        13.81        35.41 
TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X 
       63.75         1.64        50.70        20.61        30.38         8.91 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 
       53.06        37.91        47.64        18.25        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       26.56         0.69         5.56        40.41        17.06         3.22 

  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 
          21.04           20.99 
[1] "0.3 - 65.0 (21.0)" "0.7 - 63.8 (21.0)"
[1] "hr=" "1.3"
D2V2, 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
D2V3, 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
D2V4, 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"
D2V5, 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
D2V6, 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
D2V7, 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              CHOLANGIOCARCINOMA; DISTAL
  HLA-B MUTATED                            0
  HLA-B WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  HLA-B MUTATED                                     1
  HLA-B WILD-TYPE                                   2
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  HLA-B MUTATED                                  4
  HLA-B WILD-TYPE                               26
D2V8, multiclass
                                     clus
vv                                    HLA-B MUTATED HLA-B WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             1               2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  HLA-B MUTATED    4  1  0
  HLA-B WILD-TYPE 23  4  3
D2V9, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             4              23
  R1             1               4
  RX             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       0                         1     4
  HLA-B WILD-TYPE     3                         1    26
D2V10, 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(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        53.06        37.91        26.56 
TCGA-ZH-A8Y2 
       23.05 

$`MLL3 WILD-TYPE`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H 
       14.63        23.31        21.37        38.70        13.81        35.41 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X 
       21.04         1.64        50.70        20.61        30.38         8.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
       47.64        18.25        48.36         5.59         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        40.41        17.06         3.22 

  MLL3 MUTATED MLL3 WILD-TYPE 
         13.22           0.33 
  MLL3 MUTATED MLL3 WILD-TYPE 
         64.96          50.70 
  MLL3 MUTATED MLL3 WILD-TYPE 
         37.91          19.02 
[1] "13.2 - 65.0 (37.9)" "0.3 - 50.7 (19.0)" 
[1] "hr=" "6"  
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             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  MLL3 MUTATED                            1                                   0
  MLL3 WILD-TYPE                          1                                   3
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  MLL3 MUTATED                                  6
  MLL3 WILD-TYPE                               24
D3V8, multiclass
                                     clus
vv                                    MLL3 MUTATED MLL3 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     1              1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            0              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  MLL3 MUTATED    6  1  0
  MLL3 WILD-TYPE 21  4  3
D3V9, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0            6             21
  R1            1              4
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED       0                         1     6
  MLL3 WILD-TYPE     3                         1    24
D3V10, 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 = FTH1 MUTATION ANALYSIS
D4V1, 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 
       13.81        30.38        53.06 

$`FTH1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       11.15        13.22        40.11         0.33        12.66        24.36 
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       19.79        14.63        23.31        21.37        38.70        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U 
       35.41        63.75        21.04         1.64        50.70        20.61 
TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 
        8.91        37.91        47.64        18.25        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       26.56         0.69         0.85         5.56        23.05        40.41 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  FTH1 MUTATED FTH1 WILD-TYPE 
         13.81           0.33 
  FTH1 MUTATED FTH1 WILD-TYPE 
         53.06          64.96 
  FTH1 MUTATED FTH1 WILD-TYPE 
        30.380         20.825 
[1] "13.8 - 53.1 (30.4)" "0.3 - 65.0 (20.8)" 
[1] "hr=" "1.9"
D4V2, 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
D4V3, 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
D4V4, 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"
D4V5, 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
D4V6, 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
D4V7, 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             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  FTH1 MUTATED                            0                                   0
  FTH1 WILD-TYPE                          2                                   3
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  FTH1 MUTATED                                  3
  FTH1 WILD-TYPE                               27
D4V8, multiclass
                                     clus
vv                                    FTH1 MUTATED FTH1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     0              2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            0              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  FTH1 MUTATED    2  1  0
  FTH1 WILD-TYPE 25  4  3
D4V9, multiclass
    clus
vv   FTH1 MUTATED FTH1 WILD-TYPE
  R0            2             25
  R1            1              4
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FTH1 MUTATED       0                         0     3
  FTH1 WILD-TYPE     3                         2    27
D4V10, 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(5) Variable = TP53 MUTATION ANALYSIS
D5V1, 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        40.41 

$`TP53 WILD-TYPE`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        21.37        38.70        13.81        64.96        35.41 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z 
        1.64        50.70        20.61        30.38         8.91        53.06 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       37.91        47.64        18.25        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.69         0.85         5.56        23.05        17.06         3.22 

  TP53 MUTATED TP53 WILD-TYPE 
         13.22           0.33 
  TP53 MUTATED TP53 WILD-TYPE 
         63.75          64.96 
  TP53 MUTATED TP53 WILD-TYPE 
         23.31          20.20 
[1] "13.2 - 63.8 (23.3)" "0.3 - 65.0 (20.2)" 
[1] "hr=" "1.9"
D5V2, 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
D5V3, 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
D5V4, 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"
D5V5, 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
D5V6, 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
D5V7, 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             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  TP53 MUTATED                            1                                   1
  TP53 WILD-TYPE                          1                                   2
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  TP53 MUTATED                                  3
  TP53 WILD-TYPE                               27
D5V8, multiclass
                                     clus
vv                                    TP53 MUTATED TP53 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     1              1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            1              2
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  TP53 MUTATED    5  0  0
  TP53 WILD-TYPE 22  5  3
D5V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0            5             22
  R1            0              5
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0     5
  TP53 WILD-TYPE     3                         2    25
D5V10, 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(6) Variable = ARID1A MUTATION ANALYSIS
D6V1, 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 
       38.70        13.81         0.69         0.85         5.56 

$`ARID1A WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       11.15        13.22        40.11         0.33        12.66        24.36 
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2H 
       19.79        14.63        23.31        21.37        64.96        35.41 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W 
       63.75        21.04         1.64        50.70        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
        8.91        53.06        37.91        47.64        18.25        48.36 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.59        26.56        23.05        40.41        17.06         3.22 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.69             0.33 
  ARID1A MUTATED ARID1A WILD-TYPE 
           38.70            64.96 
  ARID1A MUTATED ARID1A WILD-TYPE 
            5.56            22.21 
[1] "0.7 - 38.7 (5.6)"  "0.3 - 65.0 (22.2)"
[1] "hr=" "3"  
D6V2, 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
D6V3, 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
D6V4, 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"
D6V5, 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
D6V6, 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
D6V7, 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               CHOLANGIOCARCINOMA; DISTAL
  ARID1A MUTATED                            0
  ARID1A WILD-TYPE                          2
                  vv
clus               CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  ARID1A MUTATED                                     1
  ARID1A WILD-TYPE                                   2
                  vv
clus               CHOLANGIOCARCINOMA; INTRAHEPATIC
  ARID1A MUTATED                                  4
  ARID1A WILD-TYPE                               26
D6V8, multiclass
                                     clus
vv                                    ARID1A MUTATED ARID1A WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                       0                2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR              1                2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 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"
                  vv
clus               R0 R1 RX
  ARID1A MUTATED    2  2  1
  ARID1A WILD-TYPE 25  3  2
D6V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              2               25
  R1              2                3
  RX              1                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       1                         0     4
  ARID1A WILD-TYPE     2                         2    26
D6V10, 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(7) Variable = DDHD1 MUTATION ANALYSIS
D7V1, 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 
       38.70        21.04        53.06        47.64 

$`DDHD1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       11.15        13.22        40.11         0.33        12.66        24.36 
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G 
       19.79        14.63        23.31        21.37        13.81        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W 
       35.41        63.75         1.64        50.70        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
        8.91        37.91        18.25        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.69         0.85         5.56        23.05        40.41        17.06 
TCGA-ZU-A8S4 
        3.22 

  DDHD1 MUTATED DDHD1 WILD-TYPE 
          21.04            0.33 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          53.06           64.96 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          43.17           19.79 
[1] "21.0 - 53.1 (43.2)" "0.3 - 65.0 (19.8)" 
[1] "hr=" "3.2"
D7V2, 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
D7V3, 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
D7V4, 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"
D7V5, 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
D7V6, 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
D7V7, 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              CHOLANGIOCARCINOMA; DISTAL
  DDHD1 MUTATED                            0
  DDHD1 WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DDHD1 MUTATED                                     0
  DDHD1 WILD-TYPE                                   3
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DDHD1 MUTATED                                  4
  DDHD1 WILD-TYPE                               26
D7V8, multiclass
                                     clus
vv                                    DDHD1 MUTATED DDHD1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             0               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  DDHD1 MUTATED    2  2  0
  DDHD1 WILD-TYPE 25  3  3
D7V9, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  R0             2              25
  R1             2               3
  RX             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDHD1 MUTATED       0                         0     4
  DDHD1 WILD-TYPE     3                         2    26
D7V10, 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(8) Variable = MUC2 MUTATION ANALYSIS
D8V1, 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-ZH-A8Y4 TCGA-W5-AA2H TCGA-W5-AA2O TCGA-ZD-A8I3 
       11.15        13.22        24.36        35.41        21.04         5.56 
TCGA-ZU-A8S4 
        3.22 

$`MUC2 WILD-TYPE`
TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC 
       40.11         0.33        12.66        19.79        14.63        23.31 
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2Q 
       21.37        38.70        13.81        64.96        63.75         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       50.70        20.61        30.38         8.91        53.06        37.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       47.64        18.25        48.36         5.59        26.56         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85        23.05        40.41        17.06 

  MUC2 MUTATED MUC2 WILD-TYPE 
          3.22           0.33 
  MUC2 MUTATED MUC2 WILD-TYPE 
         35.41          64.96 
  MUC2 MUTATED MUC2 WILD-TYPE 
         13.22          22.21 
[1] "3.2 - 35.4 (13.2)" "0.3 - 65.0 (22.2)"
[1] "hr=" "2.6"
D8V2, 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
D8V3, 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
D8V4, 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"
D8V5, 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
D8V6, 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
D8V7, 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             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  MUC2 MUTATED                            2                                   0
  MUC2 WILD-TYPE                          0                                   3
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  MUC2 MUTATED                                  5
  MUC2 WILD-TYPE                               25
D8V8, multiclass
                                     clus
vv                                    MUC2 MUTATED MUC2 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     2              0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            0              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  MUC2 MUTATED    6  1  0
  MUC2 WILD-TYPE 21  4  3
D8V9, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  R0            6             21
  R1            1              4
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC2 MUTATED       2                         0     5
  MUC2 WILD-TYPE     1                         2    25
D8V10, 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(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-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       11.15        13.22        40.11         0.33        12.66        24.36 
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       19.79        14.63        23.31        21.37        38.70        13.81 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W 
       35.41        63.75         1.64        50.70        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA38 TCGA-W5-AA39 
        8.91        53.06        37.91        47.64        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       26.56         0.69         5.56        23.05        40.41        17.06 
TCGA-ZU-A8S4 
        3.22 

  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         21.370 
[1] "0.8 - 65.0 (19.6)" "0.3 - 63.8 (21.4)"
[1] "hr=" "1.5"
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             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  IDH1 MUTATED                            0                                   1
  IDH1 WILD-TYPE                          2                                   2
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  IDH1 MUTATED                                  3
  IDH1 WILD-TYPE                               27
D9V8, multiclass
                                     clus
vv                                    IDH1 MUTATED IDH1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     0              2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            1              2
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  IDH1 MUTATED    3  1  0
  IDH1 WILD-TYPE 24  4  3
D9V9, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0            3             24
  R1            1              4
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0     4
  IDH1 WILD-TYPE     3                         2    26
D9V10, 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 = MUC21 MUTATION ANALYSIS
D10V1, 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        13.81         3.22 

$`MUC21 WILD-TYPE`
TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       13.22        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        23.31        21.37        38.70        64.96        35.41 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W 
       63.75        21.04         1.64        50.70        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
        8.91        53.06        37.91        47.64        18.25        48.36 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        5.59        26.56         0.69         0.85         5.56        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       40.41        17.06 

  MUC21 MUTATED MUC21 WILD-TYPE 
           3.22            0.33 
  MUC21 MUTATED MUC21 WILD-TYPE 
          13.81           64.96 
  MUC21 MUTATED MUC21 WILD-TYPE 
          11.15           22.21 
[1] "3.2 - 13.8 (11.2)" "0.3 - 65.0 (22.2)"
[1] "hr=" "4.2"
D10V2, 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
D10V3, 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
D10V4, 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"
D10V5, 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
D10V6, 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
D10V7, 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              CHOLANGIOCARCINOMA; DISTAL
  MUC21 MUTATED                            0
  MUC21 WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  MUC21 MUTATED                                     0
  MUC21 WILD-TYPE                                   3
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  MUC21 MUTATED                                  3
  MUC21 WILD-TYPE                               27
D10V8, multiclass
                                     clus
vv                                    MUC21 MUTATED MUC21 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             0               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  MUC21 MUTATED    3  0  0
  MUC21 WILD-TYPE 24  5  3
D10V9, multiclass
    clus
vv   MUC21 MUTATED MUC21 WILD-TYPE
  R0             3              24
  R1             0               5
  RX             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC21 MUTATED       1                         0     2
  MUC21 WILD-TYPE     2                         2    28
D10V10, 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(11) Variable = CLIP4 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  CLIP4 MUTATED    3  1
  CLIP4 WILD-TYPE 15 16
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              4              31 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              1              16 
$`CLIP4 MUTATED`
TCGA-W5-AA31 TCGA-W5-AA2U TCGA-W5-AA33 TCGA-ZH-A8Y5 
        0.33        20.61        47.64        40.41 

$`CLIP4 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        13.22        40.11        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        21.37        38.70        13.81        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W 
       35.41        63.75        21.04         1.64        50.70        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 
        8.91        53.06        37.91        18.25        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y6 
       26.56         0.69         0.85         5.56        23.05        17.06 
TCGA-ZU-A8S4 
        3.22 

  CLIP4 MUTATED CLIP4 WILD-TYPE 
           0.33            0.69 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
          47.64           64.96 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
          30.51           21.04 
[1] "0.3 - 47.6 (30.5)" "0.7 - 65.0 (21.0)"
[1] "hr=" "2.2"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  CLIP4 MUTATED         3        0         0        0         0         1
  CLIP4 WILD-TYPE      16        9         1        1         2         2
D11V3, multiclass
           clus
vv          CLIP4 MUTATED CLIP4 WILD-TYPE
  STAGE I               3              16
  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
  CLIP4 MUTATED    3  0  1
  CLIP4 WILD-TYPE 16 12  3
D11V4, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 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"
D11V5, binary
                 cls
clus               0  1
  CLIP4 MUTATED    3  1
  CLIP4 WILD-TYPE 22  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      3    1
  CLIP4 WILD-TYPE   22    4
   clus
vv  CLIP4 MUTATED CLIP4 WILD-TYPE
  0             3              22
  1             1               4
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus               0  1
  CLIP4 MUTATED    3  1
  CLIP4 WILD-TYPE 25  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      3    1
  CLIP4 WILD-TYPE   25    3
   clus
vv  CLIP4 MUTATED CLIP4 WILD-TYPE
  0             3              25
  1             1               3
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus               0  1
  CLIP4 MUTATED    1  3
  CLIP4 WILD-TYPE 18 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      1    3
  CLIP4 WILD-TYPE   18   13
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  FEMALE             1              18
  MALE               3              13
[1] 2 2
[1] FALSE
                 vv
clus              CHOLANGIOCARCINOMA; DISTAL
  CLIP4 MUTATED                            0
  CLIP4 WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  CLIP4 MUTATED                                     0
  CLIP4 WILD-TYPE                                   3
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  CLIP4 MUTATED                                  4
  CLIP4 WILD-TYPE                               26
D11V8, multiclass
                                     clus
vv                                    CLIP4 MUTATED CLIP4 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             0               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  CLIP4 MUTATED    4  0  0
  CLIP4 WILD-TYPE 23  5  3
D11V9, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  R0             4              23
  R1             0               5
  RX             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLIP4 MUTATED       0                         0     4
  CLIP4 WILD-TYPE     3                         2    26
D11V10, multiclass
                           clus
vv                          CLIP4 MUTATED CLIP4 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(12) Variable = BAP1 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED    4  2
  BAP1 WILD-TYPE 14 15
  BAP1 MUTATED BAP1 WILD-TYPE 
             6             29 
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             15 
$`BAP1 MUTATED`
TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2W 
        0.33        24.36        21.37        38.70        13.81        30.38 

$`BAP1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       11.15        13.22        40.11        12.66        19.79        14.63 
TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
       23.31        64.96        35.41        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       50.70        20.61         8.91        53.06        37.91        47.64 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       18.25        48.36         5.59        26.56         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        23.05        40.41        17.06         3.22 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.33           0.69 
  BAP1 MUTATED BAP1 WILD-TYPE 
         38.70          64.96 
  BAP1 MUTATED BAP1 WILD-TYPE 
        22.865         20.610 
[1] "0.3 - 38.7 (22.9)" "0.7 - 65.0 (20.6)"
[1] "hr=" "1.4"
D12V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED         3        2         0        0         1         0
  BAP1 WILD-TYPE      16        7         1        1         1         3
D12V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              3             16
  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
  BAP1 MUTATED    3  3  0
  BAP1 WILD-TYPE 16  9  4
D12V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            3             16
  T2            3              9
  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
  BAP1 MUTATED    5  1
  BAP1 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      5    1
  BAP1 WILD-TYPE   20    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            5             20
  1            1              4
[1] 2 2
[1] FALSE
D12V6, binary
                cls
clus              0  1
  BAP1 MUTATED    6  0
  BAP1 WILD-TYPE 22  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      6    0
  BAP1 WILD-TYPE   22    4
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            6             22
  1            0              4
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus              0  1
  BAP1 MUTATED    2  4
  BAP1 WILD-TYPE 17 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      2    4
  BAP1 WILD-TYPE   17   12
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            2             17
  MALE              4             12
[1] 2 2
[1] FALSE
                vv
clus             CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  BAP1 MUTATED                            0                                   0
  BAP1 WILD-TYPE                          2                                   3
                vv
clus             CHOLANGIOCARCINOMA; INTRAHEPATIC
  BAP1 MUTATED                                  6
  BAP1 WILD-TYPE                               24
D12V8, multiclass
                                     clus
vv                                    BAP1 MUTATED BAP1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                     0              2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR            0              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC               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"
                vv
clus             R0 R1 RX
  BAP1 MUTATED    4  2  0
  BAP1 WILD-TYPE 23  3  3
D12V9, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0            4             23
  R1            2              3
  RX            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED       1                         0     5
  BAP1 WILD-TYPE     2                         2    25
D12V10, multiclass
                           clus
vv                          BAP1 MUTATED BAP1 WILD-TYPE
  ASIAN                                1              2
  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(13) Variable = CDC27 MUTATION ANALYSIS
D13V1, 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-AA31 TCGA-W5-AA2W TCGA-W5-AA34 TCGA-YR-A95A 
       11.15         0.33        30.38        18.25         0.85 

$`CDC27 WILD-TYPE`
TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       13.22        40.11        12.66        24.36        19.79        14.63 
TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H 
       23.31        21.37        38.70        13.81        64.96        35.41 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2X 
       63.75        21.04         1.64        50.70        20.61         8.91 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       53.06        37.91        47.64        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.69         5.56        23.05        40.41        17.06         3.22 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.33            0.69 
  CDC27 MUTATED CDC27 WILD-TYPE 
          30.38           64.96 
  CDC27 MUTATED CDC27 WILD-TYPE 
          11.15           22.21 
[1] "0.3 - 30.4 (11.2)" "0.7 - 65.0 (22.2)"
[1] "hr=" "3.7"
D13V2, 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
D13V3, 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
D13V4, 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"
D13V5, 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
D13V6, 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
D13V7, 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              CHOLANGIOCARCINOMA; DISTAL
  CDC27 MUTATED                            0
  CDC27 WILD-TYPE                          2
                 vv
clus              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  CDC27 MUTATED                                     1
  CDC27 WILD-TYPE                                   2
                 vv
clus              CHOLANGIOCARCINOMA; INTRAHEPATIC
  CDC27 MUTATED                                  4
  CDC27 WILD-TYPE                               26
D13V8, multiclass
                                     clus
vv                                    CDC27 MUTATED CDC27 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                      0               2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR             1               2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                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"
                 vv
clus              R0 R1 RX
  CDC27 MUTATED    4  1  0
  CDC27 WILD-TYPE 23  4  3
D13V9, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0             4              23
  R1             1               4
  RX             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       1                         0     4
  CDC27 WILD-TYPE     2                         2    26
D13V10, 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(14) Variable = FAM35A MUTATION ANALYSIS
D14V1, 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-ZH-A8Y4 TCGA-W5-AA2X TCGA-ZH-A8Y2 
       24.36         8.91        23.05 

$`FAM35A WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 
       11.15        13.22        40.11         0.33        12.66        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        21.37        38.70        13.81        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U 
       35.41        63.75        21.04         1.64        50.70        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
       30.38        53.06        37.91        47.64        18.25        48.36 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y5 
        5.59        26.56         0.69         0.85         5.56        40.41 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  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           20.825 
[1] "8.9 - 24.4 (23.1)" "0.3 - 65.0 (20.8)"
[1] "hr=" "2.6"
D14V2, 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
D14V3, 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
D14V4, 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"
D14V5, 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
D14V6, 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
D14V7, 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               CHOLANGIOCARCINOMA; DISTAL
  FAM35A MUTATED                            0
  FAM35A WILD-TYPE                          2
                  vv
clus               CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  FAM35A MUTATED                                     1
  FAM35A WILD-TYPE                                   2
                  vv
clus               CHOLANGIOCARCINOMA; INTRAHEPATIC
  FAM35A MUTATED                                  2
  FAM35A WILD-TYPE                               28
D14V8, multiclass
                                     clus
vv                                    FAM35A MUTATED FAM35A WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                       0                2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR              1                2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 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"
                  vv
clus               R0 R1 RX
  FAM35A MUTATED    1  1  1
  FAM35A WILD-TYPE 26  4  2
D14V9, multiclass
    clus
vv   FAM35A MUTATED FAM35A WILD-TYPE
  R0              1               26
  R1              1                4
  RX              1                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM35A MUTATED       0                         1     2
  FAM35A WILD-TYPE     3                         1    28
D14V10, 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"

Clustering(15) Variable = PAXIP1 MUTATION ANALYSIS
D15V1, 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-ZH-A8Y4 TCGA-W5-AA2G TCGA-W5-AA2W TCGA-W5-AA2X 
       24.36        64.96        30.38         8.91 

$`PAXIP1 WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 
       11.15        13.22        40.11         0.33        12.66        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H 
       14.63        23.31        21.37        38.70        13.81        35.41 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2Z 
       63.75        21.04         1.64        50.70        20.61        53.06 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       37.91        47.64        18.25        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.69         0.85         5.56        23.05        40.41        17.06 
TCGA-ZU-A8S4 
        3.22 

  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            20.61 
[1] "8.9 - 65.0 (27.4)" "0.3 - 63.8 (20.6)"
[1] "hr=" "1.1"
D15V2, 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
D15V3, 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
D15V4, 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"
D15V5, 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
D15V6, 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
D15V7, 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               CHOLANGIOCARCINOMA; DISTAL
  PAXIP1 MUTATED                            0
  PAXIP1 WILD-TYPE                          2
                  vv
clus               CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  PAXIP1 MUTATED                                     1
  PAXIP1 WILD-TYPE                                   2
                  vv
clus               CHOLANGIOCARCINOMA; INTRAHEPATIC
  PAXIP1 MUTATED                                  3
  PAXIP1 WILD-TYPE                               27
D15V8, multiclass
                                     clus
vv                                    PAXIP1 MUTATED PAXIP1 WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                       0                2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR              1                2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 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"
                  vv
clus               R0 R1 RX
  PAXIP1 MUTATED    2  1  1
  PAXIP1 WILD-TYPE 25  4  2
D15V9, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  R0              2               25
  R1              1                4
  RX              1                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAXIP1 MUTATED       0                         0     4
  PAXIP1 WILD-TYPE     3                         2    26
D15V10, 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"
